BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|254780837|ref|YP_003065250.1| putative restriction
endonuclease S subunit [Candidatus Liberibacter asiaticus str. psy62]
         (426 letters)

Database: nr 
           14,124,377 sequences; 4,842,793,630 total letters

Searching..................................................done


Results from round 1


>gi|254780837|ref|YP_003065250.1| putative restriction endonuclease S subunit [Candidatus
           Liberibacter asiaticus str. psy62]
 gi|254040514|gb|ACT57310.1| putative restriction endonuclease S subunit [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 426

 Score =  870 bits (2248), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 426/426 (100%), Positives = 426/426 (100%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT
Sbjct: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL
Sbjct: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
           PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR
Sbjct: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL
Sbjct: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
           VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN
Sbjct: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300

Query: 301 DKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFE 360
           DKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFE
Sbjct: 301 DKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFE 360

Query: 361 DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID
Sbjct: 361 DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420

Query: 421 LRGESQ 426
           LRGESQ
Sbjct: 421 LRGESQ 426


>gi|152973654|ref|YP_001338694.1| putative restriction endonuclease S subunit [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|294496729|ref|YP_003560422.1| putative restriction endonuclease S subunit [Klebsiella pneumoniae]
 gi|150958436|gb|ABR80464.1| putative restriction endonuclease S subunit [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|293339438|gb|ADE43992.1| putative restriction endonuclease S subunit [Klebsiella pneumoniae]
          Length = 438

 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 249/444 (56%), Positives = 300/444 (67%), Gaps = 27/444 (6%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDI-IYIGLEDVESG 59
           M  YKAY  YKDSGV+WIG +P+HW+V  ++     + GR S SG D   Y   + VE  
Sbjct: 1   MSQYKAYTSYKDSGVEWIGQVPEHWEVKRLR-----HVGRYSNSGVDKKSYEDQQTVELC 55

Query: 60  T------GKYLPKDGNSRQSDTSTVSI----FAKGQILYGK-------LGPYLRKAIIAD 102
                   +++  D    Q+  S   I      KG ++  K       +G  +   +  D
Sbjct: 56  NYTDVYYNEFISDDMPFMQATASAHEIEQFTLKKGDVIITKDSEDPSDIG--IPAFVPHD 113

Query: 103 FDGI-CSTQFLVLQP-KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
             G+ C     +++   D     +   + S            G T    +   IGN P+ 
Sbjct: 114 MPGVVCGYHLTMIRALNDNYGSYIHRSIQSDHTRAHFFVESPGITRYGLNQNTIGNAPVA 173

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           +PP  EQ  I   +  ET RID L+ ++IRFIELLKEK+QAL+++ VTKGL+P+VKMKDS
Sbjct: 174 LPPPEEQATIAATLDRETARIDALVEKKIRFIELLKEKRQALITHAVTKGLDPNVKMKDS 233

Query: 221 GIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY 280
           G+EW+G VP+HWEVKPFFALV+ELNRKN  L E+NILSLSYGNIIQK ETRNMGL PESY
Sbjct: 234 GVEWIGQVPEHWEVKPFFALVSELNRKNVGLAETNILSLSYGNIIQKPETRNMGLTPESY 293

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY 340
           ETYQIV+ GE+VFRF DLQNDKRSLRSAQV +RGIITSAYMAVKPH I STY AWLMRSY
Sbjct: 294 ETYQIVESGEVVFRFTDLQNDKRSLRSAQVTQRGIITSAYMAVKPHSIGSTYFAWLMRSY 353

Query: 341 DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
           DLCKVFYAMG GLRQSLKFEDV+RLPVL+PP+ EQ +ITN IN  TARID LVEK EQSI
Sbjct: 354 DLCKVFYAMGGGLRQSLKFEDVRRLPVLIPPVGEQSEITNTINAGTARIDALVEKTEQSI 413

Query: 401 VLLKERRSSFIAAAVTGQIDLRGE 424
            LLKERR++FI AAVTGQIDLRG+
Sbjct: 414 TLLKERRAAFITAAVTGQIDLRGK 437


>gi|113477871|ref|YP_723932.1| restriction modification system DNA specificity subunit
           [Trichodesmium erythraeum IMS101]
 gi|110168919|gb|ABG53459.1| restriction modification system DNA specificity domain
           [Trichodesmium erythraeum IMS101]
          Length = 415

 Score =  293 bits (749), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 171/422 (40%), Positives = 251/422 (59%), Gaps = 19/422 (4%)

Query: 3   HYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGK 62
           +++ YP YK SGV+W+G IP+HW++  +K  + L  G +         +G E+ E G   
Sbjct: 5   NWQKYPVYKSSGVEWLGEIPEHWEMKRLKFISHLVYGDS---------LGSENREDGNIN 55

Query: 63  YLPKDGN-SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGIC-STQFLVLQPKDVL 120
               +G     S  +T+S      I+ G+ G +  K   + F   C  T +L+ Q K   
Sbjct: 56  VYGSNGMIGLHSKANTLSPV----IIVGRKGSF-GKIQYSLFPCFCIDTAYLIDQRKT-- 108

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            + L+ WL        ++ I +   +     +      +P+ PL+EQ  I   +  +  +
Sbjct: 109 KQNLK-WLCYALQILELDKISQDTGVPGLSREKAYQKLVPVSPLSEQQAIANFLDEKLAQ 167

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID  I ++ R IELLKE+K  +++  VTKG+NPDV MK SGIEW+G VP+HWEV P FA+
Sbjct: 168 IDEYIAKKQRIIELLKEQKTVIINQAVTKGINPDVSMKYSGIEWLGEVPEHWEVLPAFAV 227

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
             E    N  L+E N+LSLSYG II+K  T N GL PES+ETYQIV PG I+ R  DLQN
Sbjct: 228 FKEQCVINRDLVEKNLLSLSYGKIIRKSFTNNFGLLPESFETYQIVTPGNIILRLTDLQN 287

Query: 301 DKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFE 360
           DKRSLR   V E+GIITSAY+ + P  +   Y+  L+  YD+ K+FY+MGSG+RQ++KF+
Sbjct: 288 DKRSLRVGLVKEKGIITSAYLCLNPQNVIPEYVYTLLHIYDILKIFYSMGSGVRQNMKFK 347

Query: 361 DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           D+KRLP+  PP+ EQ +I + I  +  +I+  +  IE+ I L++E R++ I+  VTG+ID
Sbjct: 348 DLKRLPITFPPVSEQKEIVSFIEKKLEKIERSLTVIEKEIKLIQEYRTTLISETVTGKID 407

Query: 421 LR 422
           +R
Sbjct: 408 VR 409


>gi|326201377|ref|ZP_08191249.1| hypothetical protein Cpap_4212 [Clostridium papyrosolvens DSM 2782]
 gi|325988945|gb|EGD49769.1| hypothetical protein Cpap_4212 [Clostridium papyrosolvens DSM 2782]
          Length = 631

 Score =  271 bits (692), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 145/354 (40%), Positives = 217/354 (61%), Gaps = 8/354 (2%)

Query: 74  DTSTVSIFAKGQILYG-----KLGPYLRKAIIADFDGICSTQFLVLQP--KDVLPELLQG 126
           DTS+ ++  KG  ++      K G      +++D         ++ +P  KDV  +    
Sbjct: 62  DTSSQALIKKGDFVFADTSEDKGGSGNFTCLVSDSSIFAGYHTVIARPVSKDVFYKYFAY 121

Query: 127 WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
              S +   +I+    G  +       + N     P +  Q++I   +  +T +ID++I 
Sbjct: 122 LFDSQNFRAQIQQAVSGIKVFTISQGTLKNTIASFPNIDAQIVIANYLDRKTTQIDSIIA 181

Query: 187 ERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNR 246
           ++ + IELLKEK+QA++S  VT+GL+P V MKDSG++W+G +P+HWEVKP F +  E   
Sbjct: 182 DKEKLIELLKEKRQAIISEAVTRGLDPSVPMKDSGVDWIGQIPEHWEVKPLFTVAFENKA 241

Query: 247 KNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLR 306
           KN+     N+LSLSYG I++K    N GL PES+ETYQIV+ G  + R  DLQNDKRSLR
Sbjct: 242 KNSGNQCVNLLSLSYGKIVKKDIDTNFGLLPESFETYQIVEGGYTILRLTDLQNDKRSLR 301

Query: 307 SAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRL 365
           S  V E+GIITSAY+ + P   +D  +L+ L+ +YDL K+FY++G+G+RQS+ ++D+KRL
Sbjct: 302 SGFVREKGIITSAYVGLIPSDEVDGLFLSDLLHAYDLMKIFYSLGNGVRQSMNYKDLKRL 361

Query: 366 PVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           P+L+PP  EQ  I+N +  +TA ID L+   EQ + L KE R S I+ AVTG+I
Sbjct: 362 PILLPPKSEQKQISNYLRNKTAEIDDLISTTEQQVSLFKEYRQSIISEAVTGKI 415



 Score = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/221 (28%), Positives = 105/221 (47%), Gaps = 20/221 (9%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY--------IGLEDVESGTGK 62
           KDSGV WIG IP+HW+V P+  FT     +   SG   +         I  +D+++  G 
Sbjct: 213 KDSGVDWIGQIPEHWEVKPL--FTVAFENKAKNSGNQCVNLLSLSYGKIVKKDIDTNFG- 269

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
            LP+   + Q      +I     +   K    LR   + +  GI ++ ++ L P D +  
Sbjct: 270 LLPESFETYQIVEGGYTILRLTDLQNDKRS--LRSGFVRE-KGIITSAYVGLIPSDEVDG 326

Query: 123 L-LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           L L   L + D+ +   ++  G   S  ++K +  +P+ +PP +EQ  I   +  +T  I
Sbjct: 327 LFLSDLLHAYDLMKIFYSLGNGVRQS-MNYKDLKRLPILLPPKSEQKQISNYLRNKTAEI 385

Query: 182 DTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
           D LI+   + + L KE +Q+++S  VT      +K+ DS I
Sbjct: 386 DDLISTTEQQVSLFKEYRQSIISEAVT----GKIKVADSEI 422



 Score = 41.2 bits (95), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 86/203 (42%), Gaps = 17/203 (8%)

Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQK------LETRNMGLKPESY---ETY 283
           ++K  F     L+     L E+ I  +SYG +  K      +    +    ESY    + 
Sbjct: 7   KLKYLFKFGKGLSITKENLSETGIPCVSYGQVHSKYGVILDMSKHVLPFVSESYLDTSSQ 66

Query: 284 QIVDPGEIVFRFIDLQNDKR-SLRSAQVMERGIITSAYMAV--KPHGID--STYLAWLMR 338
            ++  G+ VF   D   DK  S     ++    I + Y  V  +P   D    Y A+L  
Sbjct: 67  ALIKKGDFVF--ADTSEDKGGSGNFTCLVSDSSIFAGYHTVIARPVSKDVFYKYFAYLFD 124

Query: 339 SYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           S +         SG++  ++    +K      P I  Q  I N ++ +T +ID ++   E
Sbjct: 125 SQNFRAQIQQAVSGIKVFTISQGTLKNTIASFPNIDAQIVIANYLDRKTTQIDSIIADKE 184

Query: 398 QSIVLLKERRSSFIAAAVTGQID 420
           + I LLKE+R + I+ AVT  +D
Sbjct: 185 KLIELLKEKRQAIISEAVTRGLD 207


>gi|145631519|ref|ZP_01787287.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae R3021]
 gi|144982864|gb|EDJ90381.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae R3021]
          Length = 433

 Score =  247 bits (630), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 150/432 (34%), Positives = 232/432 (53%), Gaps = 19/432 (4%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + Y +YKDSGV+W+G IP HW+ +PI+   K    +      D I + L  + +G  +Y 
Sbjct: 2   RRYERYKDSGVEWLGEIPSHWECLPIRSIFKFRNEKNDPIKTDNI-LSLS-IANGVTEYS 59

Query: 65  PKD--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
            ++  GN R+ D S+  +     I+   +   +    ++ + G  S  +  L   +    
Sbjct: 60  DENRGGNKRKDDLSSYKLAYPNDIVLNSMNVIVGAVGVSKYFGAISPVYYALSLHNQRAN 119

Query: 123 L--LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPM------------PIPPLAEQV 168
           L   +    + +  + +    +G  +   +   +  I M            PI PL EQ 
Sbjct: 120 LSYYESIFKNENFQRGLLRFGKGILIKFGENGKMNTIRMKISQDDLKKLYFPISPLDEQQ 179

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I + +  +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G V
Sbjct: 180 KIAQFLDDKTAKIDRAVELAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQV 239

Query: 229 PDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP 288
           P+HWE+     +  E  R N  + E+ +LSLSYG II K E +  GL PES+ETYQIV+P
Sbjct: 240 PEHWELTIGMNVFRENKRDNKGMKENTVLSLSYGKIIIKPEEKLFGLVPESFETYQIVEP 299

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFY 347
            +I+ R  DLQND+ SLR+    ++GIITSAY+ +K  +   + +L + + + D+ KV Y
Sbjct: 300 NDIIIRCTDLQNDQTSLRTGLAQDKGIITSAYLNLKVINNYSAKFLHYYLHALDITKVLY 359

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
             GSGLRQ+L F D KRLP++   + EQ  I + ++ +TA+ID  +      I  LKE +
Sbjct: 360 KFGSGLRQNLSFLDFKRLPIIDISLAEQQKIADYLDTQTAKIDRAIALKTAHIEKLKEYK 419

Query: 408 SSFIAAAVTGQI 419
           S  I   VTG++
Sbjct: 420 SVLINDVVTGKV 431


>gi|145629009|ref|ZP_01784808.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 22.1-21]
 gi|145639608|ref|ZP_01795212.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae PittII]
 gi|144978512|gb|EDJ88235.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 22.1-21]
 gi|145271399|gb|EDK11312.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae PittII]
 gi|162949226|gb|ABY21299.1| probable type I restriction-modification system specificity protein
           [Haemophilus influenzae]
 gi|309750476|gb|ADO80460.1| Probable type I restriction modification system, specificity
           component HsdS2 [Haemophilus influenzae R2866]
          Length = 433

 Score =  245 bits (626), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 149/432 (34%), Positives = 233/432 (53%), Gaps = 19/432 (4%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + Y +YKDSGV+W+G IP HW+ VP++   K    + +    D I + L  + +G  +Y 
Sbjct: 2   RRYERYKDSGVEWLGEIPTHWECVPLRSIFKFRNEKNNPIKTDNI-LSLS-IANGVTEYS 59

Query: 65  PKD--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
            ++  GN R+ D S+  +     I+   +   +    ++ + G  S  +  L   +    
Sbjct: 60  DENRGGNKRKDDLSSYKLAYPNDIVLNSMNVIVGAVGVSKYFGAISPVYYALSLHNQRAN 119

Query: 123 L--LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPM------------PIPPLAEQV 168
           L   +    + +  + +    +G  +   +   +  I M            PI PL EQ 
Sbjct: 120 LSYYESIFKNENFQRGLLRFGKGILIKFGENGKMNTIRMKISQDDLKKLYFPISPLDEQQ 179

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I + +  +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G V
Sbjct: 180 KIAQFLDDKTAKIDRAVELAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQV 239

Query: 229 PDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP 288
           P+HWE+     +  E  R N  + E+ +LSLSYG II K E +  GL PES+ETYQIV+P
Sbjct: 240 PEHWELTIGMNVFRENKRDNKGMKENTVLSLSYGKIIIKPEEKLFGLVPESFETYQIVEP 299

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFY 347
            +I+ R  DLQND+ SLR+    ++GIITSAY+ +K  +   + +L + + + D+ KV Y
Sbjct: 300 NDIIIRCTDLQNDQTSLRTGLAQDKGIITSAYLNLKVINNYSAKFLHYYLHALDITKVLY 359

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
             GSGLRQ+L F D KRLP++   + EQ  I + ++ +T++ID  +      I  LKE +
Sbjct: 360 KFGSGLRQNLSFLDFKRLPIIDISLAEQQQIADYLDKQTSKIDQAIALKTAHIEKLKEYK 419

Query: 408 SSFIAAAVTGQI 419
           S  I   VTG++
Sbjct: 420 SVLINDVVTGKV 431


>gi|120601537|ref|YP_965937.1| restriction modification system DNA specificity subunit
           [Desulfovibrio vulgaris DP4]
 gi|120561766|gb|ABM27510.1| restriction modification system DNA specificity domain
           [Desulfovibrio vulgaris DP4]
          Length = 438

 Score =  230 bits (586), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 110/199 (55%), Positives = 145/199 (72%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           KDSG+EW+G +P HW V   ++L +E +  N  ++ESN+LSLSYG II+K    N GL P
Sbjct: 10  KDSGVEWLGKIPSHWSVTSLYSLASECDFPNKDMLESNLLSLSYGRIIRKDINSNDGLLP 69

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLM 337
           ES+ETYQIVD G+IV R  DLQND+RSLRS  V ERGIITSAY A++P     +YLA+L+
Sbjct: 70  ESFETYQIVDHGDIVLRLTDLQNDQRSLRSGLVKERGIITSAYTAIRPTASHYSYLAYLL 129

Query: 338 RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           R+YD  K+FY+MG GLRQS+KF D++RLP+L P   EQ  I   ++ ETA+ID L+ + E
Sbjct: 130 RAYDTLKIFYSMGGGLRQSMKFSDLRRLPILKPAYSEQSAIAVFLDHETAKIDALITEQE 189

Query: 398 QSIVLLKERRSSFIAAAVT 416
           + I LLKE+R + I+ AVT
Sbjct: 190 KLIELLKEKRQAVISHAVT 208



 Score =  158 bits (399), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 138/447 (30%), Positives = 216/447 (48%), Gaps = 46/447 (10%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           + AYP+YKDSGV+W+G IP HW V  +               KD++   L  +    G+ 
Sbjct: 3   FPAYPEYKDSGVEWLGKIPSHWSVTSLYSLAS----ECDFPNKDMLESNL--LSLSYGRI 56

Query: 64  LPKDGNSRQS----DTSTVSIFAKGQILYGKLGPY------LRKAIIADFDGICSTQFLV 113
           + KD NS          T  I   G I+  +L         LR  ++ +  GI ++ +  
Sbjct: 57  IRKDINSNDGLLPESFETYQIVDHGDIVL-RLTDLQNDQRSLRSGLVKE-RGIITSAYTA 114

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
           ++P       L  +LL    T +I     G       +  +  +P+  P  +EQ  I   
Sbjct: 115 IRPTASHYSYL-AYLLRAYDTLKIFYSMGGGLRQSMKFSDLRRLPILKPAYSEQSAIAVF 173

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  ET +ID LITE+ + IELLKEK+QA++S+ VTKGL P+V MKDSG+EW+G VP+HW+
Sbjct: 174 LDHETAKIDALITEQEKLIELLKEKRQAVISHAVTKGLAPNVPMKDSGVEWLGEVPEHWK 233

Query: 234 VKPFFALVTELNRKNTKL-------IESNILSLSYGNIIQ--KLETRNMGLKPESYETYQ 284
           V      V  +   +T         IE      + G+     +L + +  + PE+ +  +
Sbjct: 234 VAKLRRFVRAVQTGSTPSASPPNTDIEDGTYWFTPGDFSGPIRLGSSSKKVPPEAIKQGE 293

Query: 285 I-VDPGEIVFRF-IDLQNDK----RSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMR 338
           + V P   VF   I     K     +L SA      II +A        ++  +LA+ + 
Sbjct: 294 VKVFPAGAVFVVSIGATLGKIGYLLTLASANQQINAIIPNA-------DVEGLFLAYSLS 346

Query: 339 S--YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
           S   ++  +  A   G+   +  E  K + + VPP+ EQ  IT  ++ +    D LV + 
Sbjct: 347 SKTSEMMNLSNASTIGI---MNQEKTKEIWLTVPPLCEQERITKFLDEDCVTSDALVNES 403

Query: 397 EQSIVLLKERRSSFIAAAVTGQIDLRG 423
           +++I LLKERRS+ I+AAVTG+ID+RG
Sbjct: 404 QRAIDLLKERRSALISAAVTGKIDVRG 430


>gi|145642021|ref|ZP_01797593.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae R3021]
 gi|145273292|gb|EDK13166.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 22.4-21]
          Length = 411

 Score =  226 bits (576), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 139/411 (33%), Positives = 220/411 (53%), Gaps = 8/411 (1%)

Query: 15  VQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSD 74
           ++W+  IP HW +   K   K    + +E  +D I     D +         +G +    
Sbjct: 1   MEWLRQIPSHWDMQRSKFIFKKVERKVNE--EDQIVTCFRDGQVTLRANRRTEGFTNALK 58

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSI 131
                   KG ++   +  +     I+D DG  +  + V  P +   +       +L ++
Sbjct: 59  EHGYQGIRKGDLVIHAMDAFTGAIGISDSDGKATPVYSVCLPHNKQKIDVYFYAYYLRNL 118

Query: 132 DVTQRIEAICEGATMSHADWK--GIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERI 189
            ++  I ++ +G      D++      + +PIPP  EQ  I + +  +T +ID  +    
Sbjct: 119 ALSGFISSLAKGIRERSTDFRYADFAELLLPIPPYLEQQQIAQFLDDKTAKIDRAVDLAE 178

Query: 190 RFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT 249
           + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HWE+     +  E  R N 
Sbjct: 179 KQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWELTIGMNVFRENKRDNK 238

Query: 250 KLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQ 309
            + E+ +LSLSYG II K E +  GL PES+ETYQIV+P +I+ R  DLQND+ SLR+  
Sbjct: 239 GMKENTVLSLSYGKIIIKPEEKLFGLVPESFETYQIVEPNDIIIRCTDLQNDQTSLRTGL 298

Query: 310 VMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVL 368
             ++GIITSAY+ +K  +   + +L + + + D+ KV Y  GSGLRQ+L F D KRLP++
Sbjct: 299 AQDKGIITSAYLNLKVINNYSAKFLHYYLHALDITKVLYKFGSGLRQNLSFLDFKRLPII 358

Query: 369 VPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
              + EQ  I + ++ +T++ID ++      I  LKE +S  I   VTG++
Sbjct: 359 DISLAEQQQIADYLDKQTSKIDQVIALKTAHIEKLKEYKSVLINDVVTGKV 409


>gi|154508213|ref|ZP_02043855.1| hypothetical protein ACTODO_00707 [Actinomyces odontolyticus ATCC
           17982]
 gi|153797847|gb|EDN80267.1| hypothetical protein ACTODO_00707 [Actinomyces odontolyticus ATCC
           17982]
          Length = 385

 Score =  210 bits (535), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 113/269 (42%), Positives = 160/269 (59%), Gaps = 1/269 (0%)

Query: 151 WKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKG 210
           W     +P+P PP   Q  I + +  ET RI+ L       I+ L   K++++   VTKG
Sbjct: 111 WANFIQVPIPFPPPEVQDSIAKYLDRETERIEELKDSIRAQIDALDSYKRSVILDAVTKG 170

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L+P+  M DS I+W+  +P +W V P      E   KN    E+N+LSLSYG II+K   
Sbjct: 171 LDPNRDMVDSKIDWIDRLPRNWNVAPLRHFFHEHKAKNLFRQETNLLSLSYGRIIRKDIG 230

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-ID 329
              GL P ++  Y IV PG+IV R  DLQND++SLR+  V ERGI+TSAY+A++ H  +D
Sbjct: 231 TVDGLLPSNFNGYNIVGPGDIVLRLTDLQNDQKSLRTGLVNERGIVTSAYIALRKHRELD 290

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           STY  +L  +YD+C+VFY MGSG+RQ L F ++ RLP++ PP+ EQ  I   +N E  +I
Sbjct: 291 STYFHYLFHTYDICRVFYNMGSGVRQGLTFSELSRLPLVAPPLDEQRRIGRFLNEEITKI 350

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           D +  K  + + LL   + S I   VTG+
Sbjct: 351 DEVQRKKRKQLDLLDAYKKSLIYEVVTGK 379



 Score = 41.2 bits (95), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 42/177 (23%), Positives = 77/177 (43%), Gaps = 13/177 (7%)

Query: 252 IESNILSLSYGNIIQKLETRNMG----LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRS 307
           +E   +S  YG I Q    +  G    +  + +   + V PG+ V      Q     L  
Sbjct: 1   MEQMTVSQQYGVIPQSEYVKKTGSHVVVVEKDFTILKAVYPGDFVIHMRSFQG---GLEL 57

Query: 308 AQVMERGIITSAYMAV--KPHGIDSTYLAWLMRSYDLCKVFYAMGSGLR--QSLKFEDVK 363
           ++V  +G  +SAY+ +   P    + Y  W+ +         +  + +R  Q++++ +  
Sbjct: 58  SEV--KGCTSSAYVMLIPGPQIHSARYYRWVFKCDGYINELRSTSNLVRDGQAMRWANFI 115

Query: 364 RLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           ++P+  PP + Q  I   ++ ET RI+ L + I   I  L   + S I  AVT  +D
Sbjct: 116 QVPIPFPPPEVQDSIAKYLDRETERIEELKDSIRAQIDALDSYKRSVILDAVTKGLD 172


>gi|78357910|ref|YP_389359.1| type I restriction-modification system, S subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78220315|gb|ABB39664.1| type I restriction-modification system, S subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 448

 Score =  209 bits (532), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 151/457 (33%), Positives = 237/457 (51%), Gaps = 43/457 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGR------TSESGKDIIYIGLE 54
           M  YKAYP YKDSGV+WIG +P+HWK+ P+K       G+       S+   ++ Y   +
Sbjct: 1   MSQYKAYPAYKDSGVEWIGQVPEHWKIAPVKYHYDARLGKMIQPAAVSDRDIEVPYHRAQ 60

Query: 55  DVESGTGKYLPKDGNSRQSDTSTVSIFA--KGQILYGKLGPYLRKAIIA---DFDGICST 109
            V+    + +  D     +    +  F+  +G +L  + G   R AI+    + + I   
Sbjct: 61  TVQ--WERIVESDIKEMWASPRDIEQFSVSEGDLLICEGGDVCRAAIVKQPPEKNMIFQK 118

Query: 110 QFLVLQPKDVLPELLQGWLL----SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLA 165
               ++ K    E   GW++     +  ++ I+ +C   T+ H     +G++  P+PP  
Sbjct: 119 SIHRIRSKG---EYGVGWVMRLMQHLRSSEWIDVLCNKNTIVHFTSDKLGSLECPLPPPD 175

Query: 166 EQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           EQ  I   +  ET RID LI ++ RFIELLKEK+QAL+++ VTKGL+P+VKMKDSG+EW+
Sbjct: 176 EQASIAAALDRETARIDALIQKKTRFIELLKEKRQALITHAVTKGLDPNVKMKDSGVEWL 235

Query: 226 GLVPDHWEVKPFFALVTELNR--KNTKLIESNILS------LSYGNIIQKLETRNMGLKP 277
           G VP+HW   P   +  E N    +   IES  +S      ++ GN+ + +  +  G   
Sbjct: 236 GEVPEHWSSVPIKYMALERNSLFLDGDWIESKDISTDGIRYITTGNVGEGV-YKEQGSGF 294

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSL-RSAQVMERG--IITSAYMAV-KPHG-IDSTY 332
            S ET+  +   E+    + +      + R+  V + G  ++TS    + +P    +  +
Sbjct: 295 ISEETFHALGCTEVYGGDVLVSRLNNPIGRACMVPDLGVRVVTSVDNVIFRPDSKFNKKF 354

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKR-----LPVLVPPIKEQFDITNVINVETA 387
           + +L  S +    ++   S L +    + + R     + V  P I+EQ  I   ++ ETA
Sbjct: 355 IVYLFSSEE----YFKHTSNLARGATMQRISRGLLGNIRVATPSIEEQTQIARFLDHETA 410

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           RID L+ K EQSI LLKERR++FI AAVTGQIDLRGE
Sbjct: 411 RIDALIGKAEQSITLLKERRAAFITAAVTGQIDLRGE 447


>gi|297581971|ref|ZP_06943891.1| restriction endonuclease S subunit [Vibrio cholerae RC385]
 gi|297533838|gb|EFH72679.1| restriction endonuclease S subunit [Vibrio cholerae RC385]
          Length = 437

 Score =  206 bits (523), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 141/435 (32%), Positives = 228/435 (52%), Gaps = 23/435 (5%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +YK+S V W+G IP HWK++P +     N    ++SGK   Y+ L     G  +Y  K
Sbjct: 4   YSEYKESRVPWLGKIPSHWKLLPCRAIVD-NQVEKNDSGKIEEYLSLM-ANIGVVRYEEK 61

Query: 67  D--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELL 124
              GN +  D +   +  +G ++   +   +    ++ F+G+CS  ++VL+PK+ + E  
Sbjct: 62  GDVGNKKPEDLTKCKLVKQGNLVINSMNYAIGSYGMSPFNGVCSPVYIVLEPKEQIVERR 121

Query: 125 QGW-LLSIDVTQRIEAICEGATMSHA---DWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
               L      Q+  A      + H     W  I    +P+PPL EQ  I   +  ET R
Sbjct: 122 YALRLFENKPMQKHLAQLGNGILQHRAAIKWDDIKPQAVPVPPLEEQRAILYFLDRETQR 181

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID+LI E++ FI+LLKEK+QAL+S+IVTKGLNP+V+M+DSGIEW+G VP HW +     L
Sbjct: 182 IDSLIAEKLTFIKLLKEKRQALISHIVTKGLNPNVEMQDSGIEWIGQVPKHWGISKVRYL 241

Query: 241 VTELNRKNT--KLIESNILSLSYGNIIQK--LETRNMGL---KPESYETYQIVDPGEIVF 293
               N  N   +        +SYG++     L  +  GL     +  + Y ++  G+++F
Sbjct: 242 GQCQNGINIGGEFFGHGTPFVSYGDVYNNTSLPEKVQGLVLSTEKDRDNYSVI-AGDVLF 300

Query: 294 RFID--LQNDKRSLRSAQVMERGIITSAYMAVKPH--GIDSTYLAWLMRSYDLCKVFYAM 349
                 ++    S      +E+ +     +  +P    ++  +  +  R+  L + F+A 
Sbjct: 301 TRTSETIEEIGFSAVCKSTIEQAVFAGFLIRFRPDEGNLEVGFSEYYFRNEKL-RAFFAK 359

Query: 350 GSGL--RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
              L  R SL  + +K++PVL+PPI EQ +I N +  E  +   +  + E++I+LLKERR
Sbjct: 360 EMNLVTRASLSQDLLKKMPVLLPPIDEQNEIANYLQAECNKFSEIFAETEKTILLLKERR 419

Query: 408 SSFIAAAVTGQIDLR 422
           +S I+AAVTG+ID+R
Sbjct: 420 TSLISAAVTGKIDVR 434



 Score = 77.0 bits (188), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 113/223 (50%), Gaps = 11/223 (4%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALV-TELNRKNTKLIESNILSLSYGNIIQKLE 269
           + P  + K+S + W+G +P HW++ P  A+V  ++ + ++  IE  +  ++   +++  E
Sbjct: 1   MTPYSEYKESRVPWLGKIPSHWKLLPCRAIVDNQVEKNDSGKIEEYLSLMANIGVVRYEE 60

Query: 270 TRNMG-LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG- 327
             ++G  KPE     ++V  G +V   ++       +        G+ +  Y+ ++P   
Sbjct: 61  KGDVGNKKPEDLTKCKLVKQGNLVINSMNYAIGSYGMSPFN----GVCSPVYIVLEPKEQ 116

Query: 328 -IDSTYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
            ++  Y   L  +  + K    +G+G+   R ++K++D+K   V VPP++EQ  I   ++
Sbjct: 117 IVERRYALRLFENKPMQKHLAQLGNGILQHRAAIKWDDIKPQAVPVPPLEEQRAILYFLD 176

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
            ET RID L+ +    I LLKE+R + I+  VT  ++   E Q
Sbjct: 177 RETQRIDSLIAEKLTFIKLLKEKRQALISHIVTKGLNPNVEMQ 219


>gi|120553175|ref|YP_957526.1| restriction modification system DNA specificity subunit
           [Marinobacter aquaeolei VT8]
 gi|120323024|gb|ABM17339.1| restriction modification system DNA specificity domain
           [Marinobacter aquaeolei VT8]
          Length = 461

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 101/203 (49%), Positives = 139/203 (68%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           K++ I W+  +P  W++ PFF+   E    N  +   N+LSLS+G I++K  T   GL P
Sbjct: 10  KNTEIPWMQRIPSSWQLLPFFSRFFERKESNKGMKSENLLSLSFGRIVRKDITTLEGLLP 69

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLM 337
            S+ETYQ+V PG IVFR  DLQNDKRSLRSA V E+GIITSAY+AV     + T+  +L 
Sbjct: 70  ASFETYQVVHPGNIVFRLTDLQNDKRSLRSAIVNEKGIITSAYLAVSAKDFNPTFSNYLF 129

Query: 338 RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           R+YDL KVFY+MG GLRQS+K++D+K LP++ P I EQ  I   ++ ETA+ID L+ + E
Sbjct: 130 RAYDLMKVFYSMGGGLRQSMKYDDMKWLPIVCPSINEQTQIARFLDHETAKIDALIREQE 189

Query: 398 QSIVLLKERRSSFIAAAVTGQID 420
           + I LL+E+R + I+ AVT  +D
Sbjct: 190 RLIELLQEKRQAVISHAVTKGLD 212



 Score =  146 bits (369), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 132/444 (29%), Positives = 213/444 (47%), Gaps = 32/444 (7%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPI-KRF---TKLNTGRTSESGKDIIY--IGLEDVE 57
           + AYP+YK++ + W+  IP  W+++P   RF    + N G  SE+   + +  I  +D+ 
Sbjct: 3   FPAYPEYKNTEIPWMQRIPSSWQLLPFFSRFFERKESNKGMKSENLLSLSFGRIVRKDIT 62

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
           +  G  LP    + Q       +F    +   K    LR AI+ +  GI ++ +L +  K
Sbjct: 63  TLEG-LLPASFETYQVVHPGNIVFRLTDLQNDKRS--LRSAIVNE-KGIITSAYLAVSAK 118

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           D  P        + D+ +   ++  G   +M + D K +   P+  P + EQ  I   + 
Sbjct: 119 DFNPTFSNYLFRAYDLMKVFYSMGGGLRQSMKYDDMKWL---PIVCPSINEQTQIARFLD 175

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE-- 233
            ET +ID LI E+ R IELL+EK+QA++S+ VTKGL+PDV MKDSG+EW+G VP HW+  
Sbjct: 176 HETAKIDALIREQERLIELLQEKRQAVISHAVTKGLDPDVPMKDSGVEWLGEVPAHWDRT 235

Query: 234 VKPFFALVTELNR-----KNTKLIESNILSLSY--GNIIQKLETRNMGLKPESYETYQIV 286
           +      + + N      K    ++   + + +  G  ++ +     G+   + E  + +
Sbjct: 236 LIKHCCYINDGNHGEEYPKGDDFVDDADIGVPFIRGGNLKDMTVTTEGMLYITAEKNRSM 295

Query: 287 DPGEIVFRFIDLQNDKRSLRSAQV---MERGIITS--AYMAVKPHGIDSTYLAWLMRSYD 341
             G +    I   N     + A +   M    + S  AY+ V+   ID  YL   + S  
Sbjct: 296 RKGRLQVGDILFVNRGEIGKLAVIPSSMNGANLNSQIAYLRVENRIIDPHYLVHYLASDT 355

Query: 342 LCKVFYAM--GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           +     A   GS L Q     D+  + V VPP  EQ  I+  +  +    +VL  +   S
Sbjct: 356 IKAEIKAAQEGSVLTQ-YPISDLAAIHVPVPPKDEQQKISTYLKEQLFSFNVLTSEASNS 414

Query: 400 IVLLKERRSSFIAAAVTGQIDLRG 423
           I LL ERRS+ I+AAVTG+ID+R 
Sbjct: 415 INLLSERRSALISAAVTGKIDVRN 438


>gi|317132744|ref|YP_004092058.1| N-6 DNA methylase [Ethanoligenens harbinense YUAN-3]
 gi|315470723|gb|ADU27327.1| N-6 DNA methylase [Ethanoligenens harbinense YUAN-3]
          Length = 689

 Score =  201 bits (512), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 106/210 (50%), Positives = 139/210 (66%), Gaps = 2/210 (0%)

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID LI++ ++  E+L+  K+ L+  I T GL+  +  K SGI+WVG +P  WEV P  A+
Sbjct: 478 IDALISDFLQQAEMLETYKRQLIINITTHGLDTALSCKSSGIDWVGEIPCDWEVFPLRAI 537

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
             E N KNT+++  N+LSLSYG IIQK    N GL P S+E YQIV+PG +V R  DLQN
Sbjct: 538 AHENNTKNTEMLSENLLSLSYGRIIQKDIETNTGLLPASFEGYQIVEPGYVVLRLTDLQN 597

Query: 301 DKRSLRSAQVMERGIITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLK 358
           DKRSLR+  V E GIITSAY+++  H   I   Y A+L+ +YDL KVFY +G G+RQSLK
Sbjct: 598 DKRSLRTGYVKETGIITSAYLSLVVHDGRILPRYFAYLLHAYDLKKVFYTLGGGVRQSLK 657

Query: 359 FEDVKRLPVLVPPIKEQFDITNVINVETAR 388
           + D K LP+LVPPI  Q  I   I  + +R
Sbjct: 658 YSDFKMLPILVPPIPTQEKIIAYIEDKISR 687



 Score = 40.4 bits (93), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 43/176 (24%), Positives = 79/176 (44%), Gaps = 21/176 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES-GKDIIYIGL-----EDVESGTGKYL 64
           K SG+ W+G IP  W+V P++     N  + +E   ++++ +       +D+E+ TG  L
Sbjct: 515 KSSGIDWVGEIPCDWEVFPLRAIAHENNTKNTEMLSENLLSLSYGRIIQKDIETNTG-LL 573

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPE 122
           P      Q       +     +   K    LR   + +  GI ++ +L L   D  +LP 
Sbjct: 574 PASFEGYQIVEPGYVVLRLTDLQNDKRS--LRTGYVKE-TGIITSAYLSLVVHDGRILPR 630

Query: 123 LLQGWLLSIDVTQRIEAICEGA--TMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
                L + D+ +    +  G   ++ ++D+K    +P+ +PP+  Q    EKIIA
Sbjct: 631 YFAYLLHAYDLKKVFYTLGGGVRQSLKYSDFK---MLPILVPPIPTQ----EKIIA 679


>gi|121997944|ref|YP_001002731.1| restriction modification system DNA specificity subunit
           [Halorhodospira halophila SL1]
 gi|121589349|gb|ABM61929.1| restriction modification system DNA specificity domain
           [Halorhodospira halophila SL1]
          Length = 429

 Score =  201 bits (510), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 145/438 (33%), Positives = 214/438 (48%), Gaps = 49/438 (11%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           + AYP+YKDSGV+W+G +P+HW V  +KR  +L +G    S          D  S  G+Y
Sbjct: 3   FPAYPEYKDSGVEWLGEVPEHWSVSALKRVARLESGDAISS----------DHISEEGEY 52

Query: 64  LPKDGNSRQSDTSTVSIFAKGQI------LYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
               GN        +  F+ G        L G+ G        A      S   +V+ P 
Sbjct: 53  AVYGGNG-------IRGFSSGYTHDGFYPLIGRQGALCGNVNYAKGRFWASEHAVVVWPG 105

Query: 118 DVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
             +     G LL S+++ Q        A       + I N+ +P+PP  EQ  I E +  
Sbjct: 106 RQIDGFWLGELLRSMNLNQ----YATSAAQPGLSVETIENLYVPVPPDEEQQKIAELLDH 161

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           ET RID LI E+ R IELLKEK+QA++S+ VTKGL+PDV MKDSG+EW+G VP HW+V  
Sbjct: 162 ETARIDALIEEQQRLIELLKEKRQAVISHAVTKGLDPDVPMKDSGVEWLGEVPAHWDVVK 221

Query: 237 FF--ALVTELN-------RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
           F   A + E          ++  L+  N +    G ++ +      G +   Y  Y    
Sbjct: 222 FVRCAKIAEGQVDPKQEPYRSMMLVAPNHIESGTGRLMARETAEEQGAESGKYYCYA--- 278

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSA--YMAVKPHGIDSTYLAWLMRSYDLCKV 345
            G++++  I     + SLR A V     + SA  Y      G+   YL W + S     +
Sbjct: 279 -GDVIYSKI-----RPSLRKACVAYEDCLCSADMYPLRAQSGVYGDYLRWTILSESFSTL 332

Query: 346 FYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            +     +    +  E ++ + + +PP +EQ  I+  +  ETARID L+E+ E  I LL+
Sbjct: 333 AFLESERVAMPKVNRESIEEIRIPMPPPEEQLQISRTLEKETARIDALMEEAESGIQLLQ 392

Query: 405 ERRSSFIAAAVTGQIDLR 422
           ERRS+ I+AAVTG+ID+R
Sbjct: 393 ERRSALISAAVTGKIDVR 410


>gi|120612012|ref|YP_971690.1| restriction modification system DNA specificity subunit [Acidovorax
           citrulli AAC00-1]
 gi|120590476|gb|ABM33916.1| restriction modification system DNA specificity domain protein
           [Acidovorax citrulli AAC00-1]
          Length = 429

 Score =  196 bits (497), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 134/415 (32%), Positives = 215/415 (51%), Gaps = 15/415 (3%)

Query: 22  PKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLP----KDGNSRQSDTST 77
           P+ W++  +K    L   R S       Y+GLE++ES TG+ +     +D          
Sbjct: 10  PEVWRLARLKFVAPLRNERMSAGSDHPGYLGLENIESWTGRIIEVESKRDDEPADQSAGL 69

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL-PELLQGWLLSIDVTQR 136
            +IF +G +L+ KL PYL KA  A  DG+ ST+ LV++P ++L P  L   +L+ D    
Sbjct: 70  ANIFREGDVLFCKLRPYLAKACHAPRDGVGSTELLVMRPSELLEPRFLLYSILTPDFVGA 129

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLK 196
           ++A   GA M  A+W  IG++ + +PPL EQ LI   +  ET  ID LI E+ R + LL+
Sbjct: 130 VDASTFGAKMPRANWDFIGSLEVKVPPLEEQRLIANYLDRETAGIDGLIAEKERMLALLE 189

Query: 197 EKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL------VTELNRKNTK 250
           EK+ AL+S +VT+GL+P+  +K SG EW+G +P HW ++    L      +T   + + +
Sbjct: 190 EKRAALISRVVTRGLDPNAPLKPSGQEWLGEIPVHWGLQRLKQLAEVRGGLTLGKQYSGE 249

Query: 251 LIESNILSLS-YGNIIQKLETRNMGLKPESYETYQIVDPGEIVFR-FIDLQNDKRSLRSA 308
           L+E   L ++   +   KL+       P S     ++  G+++     D+    R     
Sbjct: 250 LLEYPYLRVANVQDGYLKLDDVLTVEVPASEAASNLLVYGDVLMNEGGDIDKLGRGCVWR 309

Query: 309 QVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVF--YAMGSGLRQSLKFEDVKRLP 366
             +   +  +   AV+PH +DS +LA    +    + F   A  S    S+   ++K LP
Sbjct: 310 DEISPCLHQNHVFAVRPHSVDSDWLALWTSTIQAKRYFESRAKRSTNLASISGSNIKELP 369

Query: 367 VLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           V +PP+ EQ  I N + V  +R++ L  ++  S+ LL ERR++ I A VTGQI L
Sbjct: 370 VPLPPVSEQLAIQNFLAVRHSRLETLRGELRDSLRLLIERRAALITAGVTGQIPL 424



 Score = 58.2 bits (139), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 101/221 (45%), Gaps = 35/221 (15%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT---SESGK--DIIYIGLEDVESGTGKYLP 65
           K SG +W+G IP HW +  +K+  ++  G T     SG+  +  Y+ + +V+ G   YL 
Sbjct: 211 KPSGQEWLGEIPVHWGLQRLKQLAEVRGGLTLGKQYSGELLEYPYLRVANVQDG---YLK 267

Query: 66  KDGNSRQSDTSTVSI----FAKGQILYG-----------KLGPYLRKAIIADFDGICSTQ 110
            D      D  TV +     A   ++YG           KLG   R  +  D    C  Q
Sbjct: 268 LD------DVLTVEVPASEAASNLLVYGDVLMNEGGDIDKLG---RGCVWRDEISPCLHQ 318

Query: 111 --FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGAT-MSHADWKGIGNIPMPIPPLAEQ 167
                ++P  V  + L  W  +I   +  E+  + +T ++      I  +P+P+PP++EQ
Sbjct: 319 NHVFAVRPHSVDSDWLALWTSTIQAKRYFESRAKRSTNLASISGSNIKELPVPLPPVSEQ 378

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           + I+  +     R++TL  E    + LL E++ AL++  VT
Sbjct: 379 LAIQNFLAVRHSRLETLRGELRDSLRLLIERRAALITAGVT 419


>gi|38505781|ref|NP_942400.1| type I restriction-modification system S subunit [Synechocystis sp.
           PCC 6803]
 gi|38423805|dbj|BAD02014.1| type I restriction-modification system S subunit [Synechocystis sp.
           PCC 6803]
          Length = 464

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 99/211 (46%), Positives = 133/211 (63%), Gaps = 1/211 (0%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L P  + KDSG+ W+G +P HW++KP FA ++E   KNT + ES +LSLSYG I+ K   
Sbjct: 3   LKPYPEYKDSGVSWLGQIPAHWDIKPGFAFLSERKEKNTGMKESTVLSLSYGQIVVKPPE 62

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGID 329
           +  GL PES+ETYQI +PG I+ R  DLQNDK SLR  +V  RGIITSAY+ ++     +
Sbjct: 63  KLHGLVPESFETYQIAEPGNIIIRGTDLQNDKVSLRVGKVRNRGIITSAYLCLETKEKFN 122

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
             Y   L+  YDL K++Y MGSGLRQ+L F D KRLP+L PP  EQ  I   +     +I
Sbjct: 123 PDYAHLLLHGYDLMKIYYGMGSGLRQNLSFSDFKRLPLLAPPESEQSKINKYLQSIQVQI 182

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           +  +    + I LLKE++ + I  AVT  +D
Sbjct: 183 NKFIRNKRRLIELLKEQKQNIINQAVTRGLD 213



 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 117/466 (25%), Positives = 211/466 (45%), Gaps = 85/466 (18%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRF----TKLNTGRTSESGKDIIY--IGLEDVES 58
           K YP+YKDSGV W+G IP HW + P   F     + NTG    +   + Y  I ++  E 
Sbjct: 4   KPYPEYKDSGVSWLGQIPAHWDIKPGFAFLSERKEKNTGMKESTVLSLSYGQIVVKPPEK 63

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
             G  +P+   + Q       I     +   K+   LR   + +  GI ++ +L L+ K+
Sbjct: 64  LHG-LVPESFETYQIAEPGNIIIRGTDLQNDKVS--LRVGKVRN-RGIITSAYLCLETKE 119

Query: 119 VL-PELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
              P+     L   D+ +    +  G    +S +D+K    +P+  PP +EQ  I + + 
Sbjct: 120 KFNPDYAHLLLHGYDLMKIYYGMGSGLRQNLSFSDFK---RLPLLAPPESEQSKINKYLQ 176

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE-- 233
           +  V+I+  I  + R IELLKE+KQ +++  VT+GL+P+VK+K SG++W+G +P++W   
Sbjct: 177 SIQVQINKFIRNKRRLIELLKEQKQNIINQAVTRGLDPNVKLKPSGVKWIGDIPEYWSFL 236

Query: 234 -------VKPFFALVTELN---------------------RKNTKLIESNILSLS----- 260
                  VK  +A  ++                       ++  KL ES++   S     
Sbjct: 237 KLKRIACVKTGYAFKSDHYKSVGIPLIRIGDLKHSGLVDIKQAVKLQESDLTHFSCFKIQ 296

Query: 261 YGNIIQKLETRNMG-LKPESYETYQIVDPGEIVFRFID---LQNDKRSLRSAQVMERGII 316
           YG+++  +    +G +    ++T  +++     FR  +    Q+    + S++V  + + 
Sbjct: 297 YGDLLMAMTGATIGKVAKYQHQTEALLNQRVCSFRSFESKCFQDYLLFILSSEVYLKQVT 356

Query: 317 TSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQF 376
              Y   +P+  DST +++                            ++P  VPPI EQ 
Sbjct: 357 IFCYGGAQPNISDSTLMSF----------------------------KIP--VPPISEQQ 386

Query: 377 DITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            I + +  +T   D  V + E+ I L++E  +  ++  VTGQ+D+R
Sbjct: 387 AILSYVQEQTKTTDSAVSRAEREIELIQEYYTRLMSDVVTGQVDVR 432


>gi|89900160|ref|YP_522631.1| putative type I site-specific restriction-modification system, S
           subunit [Rhodoferax ferrireducens T118]
 gi|89344897|gb|ABD69100.1| putative type I site-specific restriction-modification system, S
           subunit [Rhodoferax ferrireducens T118]
          Length = 422

 Score =  193 bits (490), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 127/419 (30%), Positives = 209/419 (49%), Gaps = 15/419 (3%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG-----LEDVESGTGKYLP 65
           KDSG  WIG IP+ W++  +K     N+   ++  K ++ +      ++D+E   G   P
Sbjct: 2   KDSGAAWIGEIPQGWEIKRMKDCFISNS--RAQPNKTVLSLSYGKVIVKDMEEKKG-VTP 58

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQ 125
           +  +S Q       +     +   +    + +A      GI ++ +L +  + +      
Sbjct: 59  ESFDSYQGVHPGDVVLRLTDLQNDQKSLRVGRATTK---GIITSAYLCVSSRSLNDRYSA 115

Query: 126 GWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
             L  +   Q++     G       +  +  +   +P  AEQ  I + +  +T  ID  +
Sbjct: 116 YLLHDVGDIQKLFYGLGGGVRQSMKFADLAELLFSLPTPAEQRAIADYLDRQTALIDQRL 175

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN 245
           T       +L E ++A +   VTKGLN +  MKDSG+ W+G +P  WE+K         +
Sbjct: 176 TTLAEKKAVLAELRKATIHEAVTKGLNKNAPMKDSGVAWIGEIPQGWEIKRMKDCFISNS 235

Query: 246 RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSL 305
           R         +LSLSYG +I K      G+ PES+++YQ V PG++V R  DLQND++SL
Sbjct: 236 RAQP---NKTVLSLSYGKVIVKDMEEKKGVTPESFDSYQGVHPGDVVLRLTDLQNDQKSL 292

Query: 306 RSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY-DLCKVFYAMGSGLRQSLKFEDVKR 364
           R  +   +GIITSAY+ V    ++  Y A+L+    D+ K+FY +G G+RQS+KF D+  
Sbjct: 293 RVGRATTKGIITSAYLCVSSRSLNDRYSAYLLHDVGDIQKLFYGLGGGVRQSMKFADLAE 352

Query: 365 LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           L   +P   EQ  I + ++ +TA ID  +  +++   +LK  R + I  AVTG+IDL G
Sbjct: 353 LLFSLPTPAEQRAIADYLDRQTALIDTQLATLDEQAQVLKVLRKAIIHEAVTGKIDLSG 411



 Score =  147 bits (372), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 78/201 (38%), Positives = 115/201 (57%), Gaps = 4/201 (1%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           MKDSG  W+G +P  WE+K         +R         +LSLSYG +I K      G+ 
Sbjct: 1   MKDSGAAWIGEIPQGWEIKRMKDCFISNSRAQP---NKTVLSLSYGKVIVKDMEEKKGVT 57

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWL 336
           PES+++YQ V PG++V R  DLQND++SLR  +   +GIITSAY+ V    ++  Y A+L
Sbjct: 58  PESFDSYQGVHPGDVVLRLTDLQNDQKSLRVGRATTKGIITSAYLCVSSRSLNDRYSAYL 117

Query: 337 MRSY-DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           +    D+ K+FY +G G+RQS+KF D+  L   +P   EQ  I + ++ +TA ID  +  
Sbjct: 118 LHDVGDIQKLFYGLGGGVRQSMKFADLAELLFSLPTPAEQRAIADYLDRQTALIDQRLTT 177

Query: 396 IEQSIVLLKERRSSFIAAAVT 416
           + +   +L E R + I  AVT
Sbjct: 178 LAEKKAVLAELRKATIHEAVT 198


>gi|292490880|ref|YP_003526319.1| restriction modification system DNA specificity domain protein
           [Nitrosococcus halophilus Nc4]
 gi|291579475|gb|ADE13932.1| restriction modification system DNA specificity domain protein
           [Nitrosococcus halophilus Nc4]
          Length = 441

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 134/440 (30%), Positives = 218/440 (49%), Gaps = 35/440 (7%)

Query: 6   AYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLP 65
           +Y  YKDSGV+W+G IP HW+VVP+K    L + +      ++ YIG+E+VES TG+++ 
Sbjct: 3   SYESYKDSGVEWLGEIPSHWQVVPLKYALSLASEKVITRQSNLKYIGMENVESFTGRFI- 61

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQ 125
               +        + F  G IL+GKL PYL K  + + +G+CST+FLV + +    +  +
Sbjct: 62  ---ETASEVEGMANRFLAGDILFGKLRPYLSKVALTEVEGLCSTEFLVYRARQGSSKYFR 118

Query: 126 GWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
             + S      + A   G+ M  A    IG   +PIP   EQ  I   +  +T +I+  +
Sbjct: 119 YLMTSSSFIDLVNASTYGSKMPRASADFIGIQRIPIPTKQEQTAIAAFLDRKTAQIEQAV 178

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW---------EVKP 236
             + R I LLKE+KQ L+   VT+GLN D  M+DSG+EW+G VP HW         ++ P
Sbjct: 179 NIKERQITLLKERKQILIQNAVTRGLNSDAPMRDSGVEWIGHVPKHWKFAKLKHHIDMLP 238

Query: 237 FFALVTEL---NRKNTKLIES---NILSLSYGNIIQ--KLETRNMGLKPESYETYQIVDP 288
            FA  + L   N ++ KL+     N  +  +G ++   K E  +       Y  Y +   
Sbjct: 239 GFAFKSSLYSSNSEDIKLLRGVNVNPGNTDWGEVVYWPKKEAAD-------YSKYNLAK- 290

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV----KPHGIDSTYLAWLMRSYDLCK 344
           G++V   +D       +R + + E  +       V       G+ + Y++  + S     
Sbjct: 291 GDLVMA-MDRPWISSGIRLSLIDEEDLPCLLLQRVVRIRGKSGVCTKYVSNTLSSNIFLS 349

Query: 345 VFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
            F  M +G+    +  + +      VPP  EQ +I + I  E+A++D  +  +EQ I  L
Sbjct: 350 YFEPMLTGISVPHISTDQIGNFSCPVPPYDEQLEILDYIETESAKLDKGITLLEQQITKL 409

Query: 404 KERRSSFIAAAVTGQIDLRG 423
           KE +++ I +AVTG+I + G
Sbjct: 410 KEYKATLINSAVTGKIKVPG 429


>gi|291287374|ref|YP_003504190.1| restriction modification system DNA specificity domain protein
           [Denitrovibrio acetiphilus DSM 12809]
 gi|291287883|ref|YP_003504699.1| restriction modification system DNA specificity domain protein
           [Denitrovibrio acetiphilus DSM 12809]
 gi|290884534|gb|ADD68234.1| restriction modification system DNA specificity domain protein
           [Denitrovibrio acetiphilus DSM 12809]
 gi|290885043|gb|ADD68743.1| restriction modification system DNA specificity domain protein
           [Denitrovibrio acetiphilus DSM 12809]
          Length = 441

 Score =  186 bits (472), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 140/446 (31%), Positives = 218/446 (48%), Gaps = 31/446 (6%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIK-----RFTKLNTGRTSESGKDIIYIGLEDVES 58
           YKAYP YKDSG++W+G IP+HW +   K      F  L  G      K  + +  E ++ 
Sbjct: 3   YKAYPSYKDSGIEWLGEIPEHWAIERFKFQLRAGFEGLKIGPFGSQIKAEL-LSDEGIKV 61

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAK--------GQILYGKLGPYLRKAIIAD--FDGICS 108
              + + K+         +  +F +        G IL   +G   R  +  +    GI  
Sbjct: 62  YGQENIIKNNFDLGHRFVSEELFCELEVYETLPGDILVTMMGTAGRCQVTPEKINQGIID 121

Query: 109 TQFLVLQPKDVLPELLQGWLL--SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
           +  + L+    L      +L+  S  +  +I  + +G+ M   +   I N+   +PPL E
Sbjct: 122 SHLIRLRVNKCLLSRFCKYLINDSAYIEHQIRLMGKGSIMHGLNSTIIKNLIFILPPLKE 181

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q +I + +  +T +ID LI ++ + IE L EK+ AL+++ VTKG+NPDVKMKDSG+EW+G
Sbjct: 182 QSIILKYLDKKTAQIDELIDKKKKLIEKLDEKRTALITHAVTKGMNPDVKMKDSGVEWLG 241

Query: 227 LVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIV 286
            VP+HW++     L T + ++    +  ++LS++   I  K      G     Y  YQIV
Sbjct: 242 EVPEHWDIVKAKYLFT-IEKRIAGFLGHDVLSITQTGIKVKDIESGEGQLSMDYTKYQIV 300

Query: 287 DPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST---YLAWLMRSYDLC 343
             G+     +DL      +        G+ +  Y   +    +     YL  + R Y   
Sbjct: 301 KVGDFAMNHMDLLTGYVDISQFD----GVTSPDYRVFRLSAQNCNPQYYLYHMQRGYKE- 355

Query: 344 KVFYAMGSGLRQ----SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           K+F+  G G  Q     L  ++ K L   VPP +EQ  I   I+ ET  ID L+ K E+S
Sbjct: 356 KIFFNYGHGSAQLGRWRLPTDEFKELSFPVPPYEEQQAIAEYISSETILIDSLISKTEES 415

Query: 400 IVLLKERRSSFIAAAVTGQIDLRGES 425
           I LLKE+RS+ I AAVTG+ID+R E+
Sbjct: 416 ISLLKEKRSALITAAVTGKIDVREEA 441


>gi|284041088|ref|YP_003391018.1| restriction modification system DNA specificity domain protein
           [Spirosoma linguale DSM 74]
 gi|283820381|gb|ADB42219.1| restriction modification system DNA specificity domain protein
           [Spirosoma linguale DSM 74]
          Length = 441

 Score =  185 bits (470), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 128/432 (29%), Positives = 216/432 (50%), Gaps = 25/432 (5%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD---IIYIGLEDVESGTGKY 63
           YPQYKDSG++WIG IP HW+V  IK   K+N     ES      I Y+ +  V    G  
Sbjct: 14  YPQYKDSGLEWIGEIPAHWEVGRIKYVCKINQRSLPESTAKSFPIHYVDIGSVTLEEGIV 73

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIAD---FDGICSTQFLVLQPKD-V 119
             ++   + + +    I   G  +   +  YL+     D      I ST F VL P   +
Sbjct: 74  QTEEFEFKNAPSRARRIANAGDTIISTVRTYLKAIAFVDEQQSQFIYSTGFAVLNPLPLI 133

Query: 120 LPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
           +P+ L   + S   T+++ A  +G +    +   +G + +  PPL+EQ  I E +  +T 
Sbjct: 134 MPKFLAMAVKSDSFTEQVSANSKGMSYPAINSTELGCLAICFPPLSEQTRIAEFLDRKTA 193

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE-----WVGLVPDHWEV 234
           +ID  I ++ + IELL E++Q ++   VT+GLNP+  MKDSGI+     W+G +P HWEV
Sbjct: 194 QIDQAIAQKEQLIELLNERRQVMIHRAVTRGLNPNAPMKDSGIDRGDARWIGEIPAHWEV 253

Query: 235 KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK-PESYETYQIVDPGEIVF 293
                L TE +      +   I+S++ G  ++ ++   +  +  E +  Y+    G+I F
Sbjct: 254 SRINWLFTEKDETGYPDLPLLIVSINSGVTVRDMDDTEIRKQVAEDFNVYKRALAGDIAF 313

Query: 294 RFIDLQNDKRSLRSA--QVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMG 350
                 N  R  + A   V + G+++  Y+  +P+  ++S Y  +L ++ +    F    
Sbjct: 314 ------NKMRMWQGAVGVVPQDGLVSPDYVVARPNNFVNSAYYGFLFKTREYLAEFVKHS 367

Query: 351 SGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
            G+   R  L +ED K +  +VPP++EQ  I + +N +   +     KI++ I  L+E +
Sbjct: 368 HGIAWDRNRLYWEDFKSIFAMVPPLEEQNQIVDFLNAQNEEMSFASTKIQKQIQKLQELK 427

Query: 408 SSFIAAAVTGQI 419
           S+ I +AVTG+I
Sbjct: 428 STLINSAVTGKI 439


>gi|158520294|ref|YP_001528164.1| restriction modification system DNA specificity subunit
           [Desulfococcus oleovorans Hxd3]
 gi|158509120|gb|ABW66087.1| restriction modification system DNA specificity domain
           [Desulfococcus oleovorans Hxd3]
          Length = 413

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 101/230 (43%), Positives = 140/230 (60%), Gaps = 4/230 (1%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K YP+YKDSGV+WIG +P+ W+V  +K   K    +T+   +D IYI LE+VES TG+  
Sbjct: 2   KRYPKYKDSGVEWIGEVPEQWEVKRLKFLAKNVNEQTNTKKQDEIYIALENVESWTGRIS 61

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPE 122
           P+D  +  +  S    F    IL+GKL PYL K    +  G+C  +FLVL+  D  VLPE
Sbjct: 62  PQD--NEITFESQAKCFCSNDILFGKLRPYLAKVARPNKSGVCVGEFLVLRVLDNEVLPE 119

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
            L+  L S    + + +   GA M  ADW  I N+ +  P   EQ  I   +  +T  ID
Sbjct: 120 FLEQKLRSQWFIELVNSSTFGAKMPRADWTFISNVKLTYPSPKEQNHIASYLDHKTRLID 179

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
           TLI ++ + +ELL+E++ AL+S+ VTKGLNP  KMKD+GIEW+G VP+HW
Sbjct: 180 TLIEKKQKLVELLQEQRTALISHAVTKGLNPKTKMKDTGIEWLGKVPEHW 229



 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 52/208 (25%), Positives = 99/208 (47%), Gaps = 15/208 (7%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRK-NTKLIESNILSLSYGNIIQKLETRNMG 274
           K KDSG+EW+G VP+ WEVK    L   +N + NTK  +   ++L      + +E+    
Sbjct: 6   KYKDSGVEWIGEVPEQWEVKRLKFLAKNVNEQTNTKKQDEIYIAL------ENVESWTGR 59

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVM---ERGIITSAYMAVK--PHGID 329
           + P+  E     +     F   D+   K     A+V    + G+    ++ ++   + + 
Sbjct: 60  ISPQDNEI--TFESQAKCFCSNDILFGKLRPYLAKVARPNKSGVCVGEFLVLRVLDNEVL 117

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
             +L   +RS    ++  +   G +     +  +  + +  P  KEQ  I + ++ +T  
Sbjct: 118 PEFLEQKLRSQWFIELVNSSTFGAKMPRADWTFISNVKLTYPSPKEQNHIASYLDHKTRL 177

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           ID L+EK ++ + LL+E+R++ I+ AVT
Sbjct: 178 IDTLIEKKQKLVELLQEQRTALISHAVT 205



 Score = 47.0 bits (110), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 90/204 (44%), Gaps = 22/204 (10%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK-DGN 69
           KD+G++W+G +P+HW    ++ + ++ +G    S  D +       E+   K +P   GN
Sbjct: 215 KDTGIEWLGKVPEHWATASLRWYLRIGSGEFL-SNNDFL------TEASDQKNIPVIGGN 267

Query: 70  SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWL 128
                TS  +I  +  I  G++G       + +     +   L L   KD L + L  +L
Sbjct: 268 GVMGYTSKTNI-QEPTIAIGRVGALCGNVHLVNPPAWITDNALRLSNIKDFLIDYLSLFL 326

Query: 129 LSIDV----TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
             +D+     Q  + +  G+         I +  +PIPP+ EQ  I +     +  ID  
Sbjct: 327 GVLDLNRLANQNAQPLITGSM--------IKSQKVPIPPIPEQKDILQYCSKFSQTIDHG 378

Query: 185 ITERIRFIELLKEKKQALVSYIVT 208
           I    + I +L+E +  L+S +VT
Sbjct: 379 INTLHKQIAVLQEYRTTLISDVVT 402



 Score = 43.9 bits (102), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 37/63 (58%)

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           +K   V +PPI EQ DI    +  +  ID  +  + + I +L+E R++ I+  VTG+ID+
Sbjct: 348 IKSQKVPIPPIPEQKDILQYCSKFSQTIDHGINTLHKQIAVLQEYRTTLISDVVTGKIDV 407

Query: 422 RGE 424
           R E
Sbjct: 408 RDE 410


>gi|189425259|ref|YP_001952436.1| type I restriction-modification system specificity subunit
           [Geobacter lovleyi SZ]
 gi|189421518|gb|ACD95916.1| type I restriction-modification system specificity subunit
           [Geobacter lovleyi SZ]
          Length = 461

 Score =  182 bits (461), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 99/211 (46%), Positives = 127/211 (60%), Gaps = 1/211 (0%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L P  + ++S + W+G VP HW   P F+   E   KNT L E  +LSLSYG II K E 
Sbjct: 5   LKPYPEYRESELAWLGDVPSHWHSGPGFSAFREKKVKNTGLQEKTVLSLSYGRIIVKPED 64

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK-PHGID 329
           +  GL PES+ETYQIVDPG+I+ R  DLQNDK SLR   V  RGIITSAYM +K    + 
Sbjct: 65  KLHGLVPESFETYQIVDPGDIIIRSTDLQNDKTSLRVGIVKNRGIITSAYMCMKVTETLM 124

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
             Y   L+ + DL K+ Y +GSGLRQ+L + D KRLP+ +PPI EQ  I   +N    RI
Sbjct: 125 PEYGYQLLHTLDLTKILYGLGSGLRQNLDYSDFKRLPLSIPPIDEQTSIVRFLNHANLRI 184

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           +  +    + I LL E++   I  AVT  +D
Sbjct: 185 EKAIRAKRKVIALLNEQKQVIIHRAVTRGLD 215



 Score =  136 bits (342), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 112/430 (26%), Positives = 204/430 (47%), Gaps = 22/430 (5%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVP-IKRFTKLNTGRTSESGKDIIYIGLEDV----ESG 59
           K YP+Y++S + W+G +P HW   P    F +     T    K ++ +    +    E  
Sbjct: 6   KPYPEYRESELAWLGDVPSHWHSGPGFSAFREKKVKNTGLQEKTVLSLSYGRIIVKPEDK 65

Query: 60  TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV 119
               +P+   + Q       I     +   K    LR  I+ +  GI ++ ++ ++  + 
Sbjct: 66  LHGLVPESFETYQIVDPGDIIIRSTDLQNDKTS--LRVGIVKN-RGIITSAYMCMKVTET 122

Query: 120 L-PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           L PE     L ++D+T+ +  +  G    + D+     +P+ IPP+ EQ  I   +    
Sbjct: 123 LMPEYGYQLLHTLDLTKILYGLGSGLR-QNLDYSDFKRLPLSIPPIDEQTSIVRFLNHAN 181

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
           +RI+  I  + + I LL E+KQ ++   VT+GL+P+V++K SGI W+G +P HWE     
Sbjct: 182 LRIEKAIRAKRKVIALLNEQKQVIIHRAVTRGLDPNVQLKPSGIPWLGDIPGHWEDLRSK 241

Query: 239 ALVTELNRKNTKLIESNI-LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
            +  E++ ++    E+++ +S  YG +I   +     L  ESY   ++   G++V   + 
Sbjct: 242 YVFHEVDERSVTGTETHLSMSQKYG-LIPNSQIEERRLVSESYVGAKLCRSGDLVLNRLK 300

Query: 298 LQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKV-FYAMGSGLRQ 355
                 +L   Q    G+I+  Y   +P   + + Y   + R+   C+V       G+ Q
Sbjct: 301 AHLGVFALAPGQ----GLISPDYTVFRPARPMVARYFEAMYRT-PACRVELRKRAKGIVQ 355

Query: 356 S---LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIA 412
               L  +D   + V VPP+ EQ++I   ++ E   I+ ++   E+ I LL+E R+  IA
Sbjct: 356 GFWRLYTDDFYDIRVPVPPLDEQYEIMQYLDKELLVINTVIASTEREIDLLREYRTRLIA 415

Query: 413 AAVTGQIDLR 422
             VTG++D+R
Sbjct: 416 DVVTGKLDVR 425


>gi|327396330|dbj|BAK13752.1| type I site-specific restriction-modificationsystem, S subunit and
           related helicases [defense mechanisms] hypothetical
           protein [Pantoea ananatis AJ13355]
          Length = 451

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 138/448 (30%), Positives = 220/448 (49%), Gaps = 41/448 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY-----IGLED 55
           M  YKAYP+YKDSGV+ +  IPK W +  +K   ++      + G D++      I ++D
Sbjct: 1   MAKYKAYPEYKDSGVESLDTIPKMWSIKKLKYIFEIKKRIAGKIGFDVLSVTQKGIKIKD 60

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           +ESG G+           D S       G+     +        I+++DG+ S  + V  
Sbjct: 61  IESGEGQL--------SMDYSKYQRVYPGEFAMNHMDLLTGYVDISNYDGVTSPDYRVFA 112

Query: 116 PKDVLPELLQGWL-LSIDVTQRIEAICEGATMSH-ADWK----GIGNIPMPIPPLAEQVL 169
            +D      + +L L  D  ++      G   +H   W+        I  P P L EQ+ 
Sbjct: 113 VRDKHSFYSRYYLYLLQDGYKQRRFFHLGQGSAHLGRWRLPTEAFNEIVYPCPSLTEQIH 172

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPDV MKDSG+EW+G VP
Sbjct: 173 IASFLDHETAKIDNLIEKQRQLIELLKEKRQAVISHAVTKGLNPDVPMKDSGVEWLGEVP 232

Query: 230 DHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMG---LKPESYETY 283
           +HW V   K + + + +   K     +  IL ++  NI + +    +    + P  Y+  
Sbjct: 233 EHWIVSGFKKYLSSIVDYRGKTPNKTDEGILLVTARNIKKGVLDYTLSQEFIAPSDYKEV 292

Query: 284 Q---IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY 340
               + D G+++F        +  L     ++R  I  A   +K  G+ S    +  + +
Sbjct: 293 MGRGLPDIGDVLF------TTEAPLGEVANVDRVDIALAQRIIKFKGMASRLDNYYFKYF 346

Query: 341 DLCKVF------YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
            +   F      Y+ GS   Q +K E    L  L+PPI EQ +I   ++ E  +ID+LVE
Sbjct: 347 IMSSAFQQSLNLYSSGS-TAQGIKAERFVYLRKLLPPINEQMEIVGFLDKEITKIDILVE 405

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           +    + LL+ERR++ I+AAVTG+ID+R
Sbjct: 406 QQFVMLSLLQERRTALISAAVTGKIDVR 433


>gi|21243626|ref|NP_643208.1| type I restriction-modification system specificity determinant
           [Xanthomonas axonopodis pv. citri str. 306]
 gi|21109201|gb|AAM37744.1| type I restriction-modification system specificity determinant
           [Xanthomonas axonopodis pv. citri str. 306]
          Length = 426

 Score =  180 bits (456), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 128/423 (30%), Positives = 206/423 (48%), Gaps = 19/423 (4%)

Query: 10  YKDSGVQWIGAIPKHWKVVPIKRFTKLN--TGRTSESGKDIIYIGLEDVESGTGKYLPKD 67
           +K SG  W+G +P HW V P+    +    TG   E+   +        + G  +   +D
Sbjct: 10  FKSSGAPWLGNVPTHWVVKPLWSMYRQKKITGYPEETLLSVYR------DHGVIEKSSRD 63

Query: 68  GNSRQS--DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELL 124
            N  ++  D S   +   G ++  K+  +     ++   GI S  + V     D     L
Sbjct: 64  DNKNRASEDLSGYQLVVDGDLVTNKMKTWQGSIAVSSLRGIVSPAYYVYTKLHDGNNAYL 123

Query: 125 QGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAEQVLIREKIIAETVRID 182
              L S+      ++I +G  +   D +       P+ IPP  EQ  I   +   T RID
Sbjct: 124 HHLLRSVPYITGYQSISKGIRVGQWDLEADKFRLFPVLIPPRPEQDAIVAHLDRATTRID 183

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
            L+ ++  FIELL+EK+QA++++ VTKGL+    MKDSG+EW+G VP  W+  P  + + 
Sbjct: 184 ALVAKKTHFIELLREKRQAMITHAVTKGLDRGAPMKDSGVEWLGEVPVTWDTAPLKSFL- 242

Query: 243 ELNRK--NTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
           +L R    T    + +LSL+   +I++      G  P S++ YQ +  GE+VF   D+  
Sbjct: 243 QLRRDIVGTASANTRLLSLTLQGVIERDLENPTGKMPASFDGYQRISAGEMVFCLFDMDE 302

Query: 301 DKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKF 359
             R++  AQ  + G++T AY   +P   + + YL +     D  K       GLR++++ 
Sbjct: 303 TPRTVGVAQ--QDGMLTGAYTVFRPQSDLWARYLYYFFLHVDEYKRLKPFYKGLRKTIRP 360

Query: 360 EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
                + V  P   E   I   ++  T+RID L+ K E+SI LL+E R++ I AAVTG+I
Sbjct: 361 GPFLSIQVPRPRDGEAEAIVAHLDRATSRIDTLIAKTERSIELLREHRTALITAAVTGKI 420

Query: 420 DLR 422
           DLR
Sbjct: 421 DLR 423


>gi|124515150|gb|EAY56661.1| probable restriction endonuclease, S subunit [Leptospirillum
           rubarum]
          Length = 232

 Score =  179 bits (455), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 97/232 (41%), Positives = 143/232 (61%), Gaps = 8/232 (3%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           +  YP+YKDSGV+W+G +P+HW+V  +K    L+T R  E  K    + LE++ES TG++
Sbjct: 6   WPPYPKYKDSGVEWLGELPEHWEVKKLKYCLLLST-RKIEPQKS--QVALENIESWTGRF 62

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP-E 122
           +  +        +    F +G IL+GKL PYL K  +A F G     F V++P       
Sbjct: 63  IETETKFEGDGIA----FEEGDILFGKLRPYLAKVFLAQFSGEAVGDFFVMRPFPTTDGR 118

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
            +Q  +L+      I++   GA M   DW+ +GN+ + +P L+EQ+ I   +  ET RID
Sbjct: 119 FIQYQILNKTFISIIDSSTFGAKMPRVDWEFMGNMELTLPSLSEQLAIASFLDRETSRID 178

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
           TLI+E+ R I LL+E +QAL+S+ VTKGL+P VKMKDSG+EW+G VP+HWE+
Sbjct: 179 TLISEKERLISLLQEYRQALISHAVTKGLDPKVKMKDSGVEWLGEVPEHWEI 230



 Score = 60.8 bits (146), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 102/226 (45%), Gaps = 43/226 (19%)

Query: 213 PDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRK----NTKLIESNILSLSYGNIIQKL 268
           P  K KDSG+EW+G +P+HWEVK     +    RK     +++   NI S + G  I+  
Sbjct: 8   PYPKYKDSGVEWLGELPEHWEVKKLKYCLLLSTRKIEPQKSQVALENIESWT-GRFIET- 65

Query: 269 ETRNMG--------------LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERG 314
           ET+  G              L+P   + +     GE V  F  ++    +    + ++  
Sbjct: 66  ETKFEGDGIAFEEGDILFGKLRPYLAKVFLAQFSGEAVGDFFVMRPFPTT--DGRFIQYQ 123

Query: 315 IITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKE 374
           I+   ++++    IDS+     M   D                 +E +  + + +P + E
Sbjct: 124 ILNKTFISI----IDSSTFGAKMPRVD-----------------WEFMGNMELTLPSLSE 162

Query: 375 QFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           Q  I + ++ ET+RID L+ + E+ I LL+E R + I+ AVT  +D
Sbjct: 163 QLAIASFLDRETSRIDTLISEKERLISLLQEYRQALISHAVTKGLD 208


>gi|310826741|ref|YP_003959098.1| hypothetical protein ELI_1147 [Eubacterium limosum KIST612]
 gi|308738475|gb|ADO36135.1| hypothetical protein ELI_1147 [Eubacterium limosum KIST612]
          Length = 415

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 92/202 (45%), Positives = 128/202 (63%), Gaps = 1/202 (0%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL 275
           K KDSGIEW+G VP HW V   + LVT++  KN  L E N+LSLSYG I +K      GL
Sbjct: 14  KTKDSGIEWIGSVPSHWRVHTLYQLVTQVKEKNGNLQEKNLLSLSYGKIKRKDIDSPDGL 73

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLA 334
            P S++ Y I++ G+IV R  DLQND  SLR     ERGIITSAY  ++P    +S YL 
Sbjct: 74  LPASFDGYNIIEDGDIVLRLTDLQNDHTSLRVGLATERGIITSAYTTLRPIDTSNSKYLF 133

Query: 335 WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           +L+ ++DL K FY MGSG+RQ L + +VK L +++P   E+  I   ++ + A+ID L+E
Sbjct: 134 YLLHAFDLKKGFYGMGSGVRQGLNYAEVKELRIVLPRQDEKDTIVQFLDEQCAQIDTLIE 193

Query: 395 KIEQSIVLLKERRSSFIAAAVT 416
           + + S+   K+ R+S +  AVT
Sbjct: 194 EAKLSVAEYKKWRASIVFEAVT 215



 Score =  102 bits (255), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 103/431 (23%), Positives = 190/431 (44%), Gaps = 38/431 (8%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRF-TKLNTGRTSESGKDIIYIGL-----E 54
           M     Y + KDSG++WIG++P HW+V  + +  T++     +   K+++ +       +
Sbjct: 6   MSEITTYEKTKDSGIEWIGSVPSHWRVHTLYQLVTQVKEKNGNLQEKNLLSLSYGKIKRK 65

Query: 55  DVESGTGKYLPK--DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           D++S  G  LP   DG +   D   V      Q  +  L     +  +A   GI ++ + 
Sbjct: 66  DIDSPDG-LLPASFDGYNIIEDGDIVLRLTDLQNDHTSL-----RVGLATERGIITSAYT 119

Query: 113 VLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
            L+P D        +LL + D+ +    +  G      ++  +  + + +P   E+  I 
Sbjct: 120 TLRPIDTSNSKYLFYLLHAFDLKKGFYGMGSGVRQG-LNYAEVKELRIVLPRQDEKDTIV 178

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
           + +  +  +IDTLI E    +   K+ + ++V   VTKGLNP  +MKDS I+W+G +P H
Sbjct: 179 QFLDEQCAQIDTLIEEAKLSVAEYKKWRASIVFEAVTKGLNPLAEMKDSHIDWIGQMPTH 238

Query: 232 WEVKPFFALVTELNRKN---TKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP 288
           W +     L +    KN    ++ E+    +  GN I+             Y  Y     
Sbjct: 239 WGILSLKYLCSMQAGKNLVSDQIDEAGEYPVYGGNGIRGY-----------YSKYNYEGE 287

Query: 289 GEIVFRFIDLQNDKRSLRSA-QVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFY 347
             +V R   L  +   ++      E  ++T         G++ ++L +L+   +L +  Y
Sbjct: 288 YLLVGRQGALCGNVHKIKGCFWATEHAVVTK-----NVEGVELSFLYYLLNGMNLNR--Y 340

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
           A  S  +  L    ++ +  + PPI+EQ +I+  +N     ID ++E  +  I  L+  +
Sbjct: 341 ASNSAAQPGLSVNTIQNIKTVFPPIEEQIEISTYLNDICHSIDSIIENKQSLIFELESYK 400

Query: 408 SSFIAAAVTGQ 418
            S I   VTG+
Sbjct: 401 KSLIFETVTGK 411


>gi|324991451|gb|EGC23384.1| restriction modification system DNA specificity subunit
           [Streptococcus sanguinis SK353]
          Length = 408

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 88/208 (42%), Positives = 132/208 (63%), Gaps = 2/208 (0%)

Query: 215 VKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMG 274
            +MK+SGI+W+G +P+ WEV     +  E  +KN    E N+LSLSYG II+K    + G
Sbjct: 2   TRMKESGIDWIGQIPEEWEVAKVNHIFEEHKQKNRGNKEKNLLSLSYGRIIRKSIDSSFG 61

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDS--TY 332
           L PES++TY I+  G+IV R  DLQNDKRSLR     E GIITSAY+ ++   ++S  +Y
Sbjct: 62  LLPESFDTYNIIQRGDIVLRLTDLQNDKRSLRVGLARENGIITSAYLTLRLKNLESNDSY 121

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           + +L+ +YD+CKVFY  G G+RQ   + D+ ++ +L+PP  EQ  I + ++ + A++D  
Sbjct: 122 MYYLLHTYDICKVFYNFGGGVRQGGTWSDIYKMELLIPPCNEQQKIADYLDKKIAQLDRA 181

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQID 420
              +E+ I  LK+ R+S I   VT  +D
Sbjct: 182 KRLLEKQIQKLKDYRASLIYETVTKGLD 209



 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 107/434 (24%), Positives = 187/434 (43%), Gaps = 59/434 (13%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRF----TKLNTGRTSESGKDIIY--IGLEDVESGTGKYL 64
           K+SG+ WIG IP+ W+V  +        + N G   ++   + Y  I  + ++S  G  L
Sbjct: 5   KESGIDWIGQIPEEWEVAKVNHIFEEHKQKNRGNKEKNLLSLSYGRIIRKSIDSSFG-LL 63

Query: 65  PKDGNSRQSDTSTVSIFAKGQILY--GKLGPYLR--KAIIADFDGICSTQFLVLQPKDVL 120
           P+  +       T +I  +G I+     L    R  +  +A  +GI ++ +L L+ K++ 
Sbjct: 64  PESFD-------TYNIIQRGDIVLRLTDLQNDKRSLRVGLARENGIITSAYLTLRLKNLE 116

Query: 121 P-ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE---KIIA 176
             +    +LL      ++     G       W  I  + + IPP  EQ  I +   K IA
Sbjct: 117 SNDSYMYYLLHTYDICKVFYNFGGGVRQGGTWSDIYKMELLIPPCNEQQKIADYLDKKIA 176

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV-- 234
           +  R   L+ ++I   + LK+ + +L+   VTKGL+  V MKDSGI+W+G VP+ W V  
Sbjct: 177 QLDRAKRLLEKQI---QKLKDYRASLIYETVTKGLDKTVPMKDSGIDWIGQVPEGWGVSR 233

Query: 235 -KPFFALVT--ELNRKNTKLIESNILSLSYGNIIQKLE-------TRNMGLKPESYETYQ 284
            K FF +    +++ +NT  ++    +  Y  I   LE       T N   + +      
Sbjct: 234 LKYFFDIYAGGDIDERNT--VDEYSENHPYPVISNSLENEGILGYTNNFRFQGDCVTVTG 291

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK 344
             D G+ V+R I      R L     ++               +D  +  + + S  + K
Sbjct: 292 RGDVGKAVYRNIKFYPVVRLLVCTPKIQ---------------VDCRFATYWINSAIIEK 336

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
              A+       L  + +  L     P  EQ  I + ++ +T +ID L++   Q I  + 
Sbjct: 337 NQTAVS-----QLTIQMLGELIFTNVPYVEQKKIADFLDKKTVQIDKLIQIKNQQIKNIN 391

Query: 405 ERRSSFIAAAVTGQ 418
           ++R + I   VTG+
Sbjct: 392 KQRQTLIYDYVTGK 405


>gi|299531531|ref|ZP_07044937.1| type I restriction-modification system, S subunit [Comamonas
           testosteroni S44]
 gi|298720494|gb|EFI61445.1| type I restriction-modification system, S subunit [Comamonas
           testosteroni S44]
          Length = 460

 Score =  177 bits (448), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 133/461 (28%), Positives = 216/461 (46%), Gaps = 58/461 (12%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES--------------GKDII 49
           +  YP YKDSGV+W+G +P HW V P+KR   +  G+  +S                +I 
Sbjct: 3   FPRYPAYKDSGVEWLGEVPAHWIVAPLKRGFSVTLGKMLQSDSSGPEDELLPYLRAANIQ 62

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           + G++  +       P+D                G +L  + G   R  + AD    CS 
Sbjct: 63  WTGIDASDIKQMWLSPRD--------RVQLALQLGDLLVSEGGDVGRSCLWADEIANCSF 114

Query: 110 QFLVLQPKDVL---PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
           Q  V + +         L  W+ +I     ++ +C  +T++H   + +  +P+P P   E
Sbjct: 115 QNSVNRVRATHGGSTRFLYYWMSTIKDKGYVDVLCNKSTIAHFTAEKVAAVPVPFPLPPE 174

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q  I   +  ET +ID L+ E+ + I LL+EK+QA++S+ VTKGLNP+  MKDSG+EW+ 
Sbjct: 175 QTAIVRFLDHETAKIDALVAEQEKLIALLQEKRQAVISHAVTKGLNPNAPMKDSGVEWLR 234

Query: 227 LVPDHWEVKPF--FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL---KPESYE 281
            VP HWEV         T+      + +E  I   S    I+++++R + L   K  +  
Sbjct: 235 EVPVHWEVTALKRHWTATDCKHVTAEFVEDGIPLAS----IREVQSRWVELGEAKRTTEH 290

Query: 282 TYQIV-------DPGEIVF-------RFIDLQNDKRSLRSAQ--VMERGIITSAYMAVKP 325
            YQ++        PG+++F           +  D +     Q  V+ R I  +       
Sbjct: 291 FYQLLIEGGRDPRPGDLIFSRNATVGEVAQVHQDHQPFAMGQDVVLLRRITEATSPDFLQ 350

Query: 326 HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
             I S+    +M    LC V    GS  ++ +  E+++ L +  PP  EQ  I N +  +
Sbjct: 351 LAIRSSV---VMLQLSLCMV----GSTFKR-INVEEIRSLVLAFPPPDEQIKIANHLLAQ 402

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
               D L+ +   +I LL+ERR++ I+AAVTGQID+RG +Q
Sbjct: 403 AESFDSLMTEARTAIALLQERRTALISAAVTGQIDVRGWAQ 443


>gi|327184406|gb|AEA32851.1| type i site-specific restriction-modification system, s subunit
           [Lactobacillus amylovorus GRL 1118]
          Length = 425

 Score =  177 bits (448), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 94/204 (46%), Positives = 134/204 (65%), Gaps = 1/204 (0%)

Query: 214 DVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNM 273
           + K+KDS IEW+G +P +W+VKP +    E   KN K  E N+LSLSYG IIQK      
Sbjct: 3   NSKLKDSNIEWLGKIPSNWKVKPLYLFFFERKNKNNKGKEKNLLSLSYGKIIQKDINSTG 62

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTY 332
           GL P+SY TY +++ G+I+ R  DLQNDK SLR+A   E GIITSAY+ + P    +S Y
Sbjct: 63  GLLPQSYNTYNVIEAGDIIIRPTDLQNDKHSLRTAFSKEHGIITSAYIDLAPLKDTNSEY 122

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
             +++ +YD+ KVFY MG+G+RQ L + +  +L + +P  +EQ +I N +N + ++ID L
Sbjct: 123 FHYVLHAYDIEKVFYNMGNGVRQGLNYSEFSKLKLPIPSSEEQKEIVNFLNNQVSQIDKL 182

Query: 393 VEKIEQSIVLLKERRSSFIAAAVT 416
            +KI+Q I+ L+E R S I  AVT
Sbjct: 183 SKKIQQEIIDLEEYRKSIITKAVT 206



 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 109/433 (25%), Positives = 196/433 (45%), Gaps = 50/433 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRF---------TKLNTGRTSESGKDIIYIGLEDVESGTG 61
           KDS ++W+G IP +WKV P+  F                 S S   II    +D+ S TG
Sbjct: 7   KDSNIEWLGKIPSNWKVKPLYLFFFERKNKNNKGKEKNLLSLSYGKIIQ---KDINS-TG 62

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPY--------LRKAIIADFDGICSTQFLV 113
             LP+  N       T ++   G I+   + P         LR A   +  GI ++ ++ 
Sbjct: 63  GLLPQSYN-------TYNVIEAGDII---IRPTDLQNDKHSLRTAFSKEH-GIITSAYID 111

Query: 114 LQP-KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
           L P KD   E     L + D+ +    +  G      ++     + +PIP   EQ  I  
Sbjct: 112 LAPLKDTNSEYFHYVLHAYDIEKVFYNMGNGVRQG-LNYSEFSKLKLPIPSSEEQKEIVN 170

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
            +  +  +ID L  +  + I  L+E ++++++  VTKGLNP+V MKDSGI W+G +P +W
Sbjct: 171 FLNNQVSQIDKLSKKIQQEIIDLEEYRKSIITKAVTKGLNPNVPMKDSGIPWIGKIPQNW 230

Query: 233 EV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET-YQIVDP 288
           ++   K  F L+++  +K+ ++    I     G +  +++ R  G      E  YQ +D 
Sbjct: 231 KIIKGKYLFRLLSKPVKKDDQV----ITCFRDGQVTLRVKRRTTGFTMSDQEIGYQGIDK 286

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYA 348
           G++V   +D       +  +    RG   S  + V     D  Y+ + +R+     VF A
Sbjct: 287 GDLVVHGMDGFAGAIGISDS----RG-KGSPVLNVLDSNQDKKYMMYCLRATAQLGVFQA 341

Query: 349 MGSGLR---QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
           +  G+R      ++  +  L   +PP  EQ ++ N ++  + +++ +++  +  +  L +
Sbjct: 342 LAKGIRVRSADTRWPTLANLKYAIPPQSEQANVVNYLSNNSYKLNAIIQAKKDLVEKLNQ 401

Query: 406 RRSSFIAAAVTGQ 418
            + S I   VTG+
Sbjct: 402 YKQSIIYEYVTGK 414


>gi|229847074|ref|ZP_04467180.1| type I restriction-modification system S subunit [Haemophilus
           influenzae 7P49H1]
 gi|229810158|gb|EEP45878.1| type I restriction-modification system S subunit [Haemophilus
           influenzae 7P49H1]
          Length = 434

 Score =  176 bits (447), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 92/200 (46%), Positives = 129/200 (64%), Gaps = 1/200 (0%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           KDSG+EW+G +P +W++     +  E  R N  + E  +LSLSYG II K E + +GL P
Sbjct: 8   KDSGVEWLGKIPSYWDLTIGMNVFRENKRDNKGMKEKTVLSLSYGQIIIKPEEKLVGLVP 67

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWL 336
           ES+ETYQIV P +I+ R  DLQND+ SLR+    ++GIITSAY+ +K  +   + +L + 
Sbjct: 68  ESFETYQIVKPNDIIIRCTDLQNDQTSLRTGLAKDKGIITSAYLNLKVINNHSAKFLHYY 127

Query: 337 MRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
           + + D+ KV Y  GSGLRQ+L F D KRLP++  P+ EQ  I   +N +TA+ID  V+  
Sbjct: 128 LHTLDITKVLYKFGSGLRQNLSFLDFKRLPIIDIPLSEQQKIAQFLNDKTAKIDQAVDLA 187

Query: 397 EQSIVLLKERRSSFIAAAVT 416
           E+ IVLLKE +   I  AVT
Sbjct: 188 EKQIVLLKEHKQILIQNAVT 207



 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 120/458 (26%), Positives = 203/458 (44%), Gaps = 66/458 (14%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVV----PIKRFTKLNTGRTSESGKDIIY--IGLEDVES 58
           + Y  YKDSGV+W+G IP +W +       +   + N G   ++   + Y  I ++  E 
Sbjct: 2   RRYESYKDSGVEWLGKIPSYWDLTIGMNVFRENKRDNKGMKEKTVLSLSYGQIIIKPEEK 61

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-K 117
             G  +P+   + Q       I     +   +    LR  +  D  GI ++ +L L+   
Sbjct: 62  LVG-LVPESFETYQIVKPNDIIIRCTDLQNDQTS--LRTGLAKD-KGIITSAYLNLKVIN 117

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           +   + L  +L ++D+T+ +     G    +S  D+K    +P+   PL+EQ  I + + 
Sbjct: 118 NHSAKFLHYYLHTLDITKVLYKFGSGLRQNLSFLDFK---RLPIIDIPLSEQQKIAQFLN 174

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HW VK
Sbjct: 175 DKTAKIDQAVDLAEKQIVLLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWNVK 234

Query: 236 P------------------FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
                              F   V E  R+          S    N+ Q ++  N+    
Sbjct: 235 KLKYMGYLYSGLTGKSADDFSKEVKEGFREFVPFTTICNFSQIKENVFQYVKVMNL---- 290

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDS------- 330
              E   IV   +++F           L S++ +E    +S Y+  +   ++S       
Sbjct: 291 ---ENQNIVKKHDLLF-----------LMSSETLEDIAKSSVYLLDQESFLNSFCKGFRF 336

Query: 331 ------TYLAWLMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
                  ++ +L+ S +    F  +G G  R ++K E V  + VL+PP  EQ  I + ++
Sbjct: 337 IEKHSSIFINYLINSNNYRAYFNLVGRGFTRINIKQEFVNSVYVLLPPFSEQQKIADYLD 396

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            +T +ID  +      I  LKE +S  I   VTG++ +
Sbjct: 397 KQTTKIDQAIALKTAHIEKLKEYKSVLINNVVTGKVQV 434


>gi|225076790|ref|ZP_03719989.1| hypothetical protein NEIFLAOT_01841 [Neisseria flavescens
           NRL30031/H210]
 gi|224951888|gb|EEG33097.1| hypothetical protein NEIFLAOT_01841 [Neisseria flavescens
           NRL30031/H210]
          Length = 430

 Score =  176 bits (445), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 91/200 (45%), Positives = 128/200 (64%), Gaps = 1/200 (0%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           KDSG+EW+G +P  WE+     +  E  R N  + E  +LSLSYG II K E + +GL P
Sbjct: 8   KDSGVEWLGKIPSQWELTIGMNVFRENKRDNKGMKEKTVLSLSYGQIIIKPEEKLVGLVP 67

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWL 336
           ES+ETYQIV+P +I+ R  DLQND+ SLR+    ++GIITSAY+ +K  +   + +L + 
Sbjct: 68  ESFETYQIVEPNDIIIRCTDLQNDQTSLRTGLAKDKGIITSAYLNLKVINNHSAKFLHYY 127

Query: 337 MRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
           + + D+ KV Y  GSGLRQ+L F D KRLP++  P+ EQ  I   ++ +TA+ID  V+  
Sbjct: 128 LHTLDITKVLYKFGSGLRQNLSFLDFKRLPIIDIPLSEQQKIAQFLDDKTAKIDQAVDLA 187

Query: 397 EQSIVLLKERRSSFIAAAVT 416
           E+ I LLKE +   I  AVT
Sbjct: 188 EKQIALLKEHKQILIQNAVT 207



 Score =  109 bits (272), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 121/450 (26%), Positives = 203/450 (45%), Gaps = 58/450 (12%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVV----PIKRFTKLNTGRTSESGKDIIY--IGLEDVES 58
           + Y  YKDSGV+W+G IP  W++       +   + N G   ++   + Y  I ++  E 
Sbjct: 2   RRYESYKDSGVEWLGKIPSQWELTIGMNVFRENKRDNKGMKEKTVLSLSYGQIIIKPEEK 61

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-K 117
             G  +P+   + Q       I     +   +    LR  +  D  GI ++ +L L+   
Sbjct: 62  LVG-LVPESFETYQIVEPNDIIIRCTDLQNDQTS--LRTGLAKD-KGIITSAYLNLKVIN 117

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           +   + L  +L ++D+T+ +     G    +S  D+K    +P+   PL+EQ  I + + 
Sbjct: 118 NHSAKFLHYYLHTLDITKVLYKFGSGLRQNLSFLDFK---RLPIIDIPLSEQQKIAQFLD 174

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HW VK
Sbjct: 175 DKTAKIDQAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWSVK 234

Query: 236 PFFALVTELNRKNTKLIESNILSLSYGNI-----IQKLETRNMGLKPESYETYQIVDPGE 290
                     +  T  I S I  L  G+      I  L ++N+      ++   + D   
Sbjct: 235 KI--------KHVTSKIGSGITPLGGGSNYIDGGIPLLRSQNI-----HFDRIDLNDVAR 281

Query: 291 IV-FRFIDLQNDKRSLRSAQVM-----------------ERGIITSAYMAVKPH-GIDST 331
           I  F    ++N K  +R   V+                 E   +      ++P+  I++ 
Sbjct: 282 ISEFTHNSMKNSK--VRKGDVLLNITGGSLGRCFYVDSNEEMNVNQHVCIIRPNKKINTI 339

Query: 332 YLAWLMRSYDLCKV--FYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           +L  L+ S    K   F+  G G R+ L F+ +K   + +P +KEQ  I   ++ + A+I
Sbjct: 340 FLNMLLASEVGQKQIWFFQQGGG-REGLNFQAIKNFYLPLPDLKEQQKIAIYLDKQVAKI 398

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           D  +      I  LKE +S  I   VTG++
Sbjct: 399 DQAIALKTAHIEKLKEYKSVLINDVVTGKV 428


>gi|315180942|gb|ADT87856.1| type I restriction-modification system specificity determinant
           [Vibrio furnissii NCTC 11218]
          Length = 449

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 138/448 (30%), Positives = 232/448 (51%), Gaps = 39/448 (8%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M  Y++YP+YKDSG++W+G IP  W  +P+ R     T R+  S K+++      V    
Sbjct: 1   MGKYQSYPKYKDSGIEWMGDIPNEWVTIPVGRLY-YRTKRSGHSEKELL-----SVYRDY 54

Query: 61  GKYLPK----DGNSRQSDTST-VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           G  +PK    D N+++SD  T   +     ++  K+  +     +++++GI S  + V +
Sbjct: 55  G-VIPKSSRDDNNNKESDDLTPYQLVQPNDLVMNKMKAWQGSIAVSEYEGIVSPAYFVYE 113

Query: 116 PKDVLPELLQ----GWLLS--IDVTQRIEAICEGATMSHADWK--GIGNIPMPIPPLAEQ 167
           P++ L EL       +LL   I +TQ + +  +G  ++  D        I + +P   EQ
Sbjct: 114 PREKLFELAHPRYVHYLLRNPIYITQYM-SRSKGIRVNQWDLDPDEFKTIELLLPSKDEQ 172

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I E +  ET +ID+LI ++ + I+LLKEK+QA++S+ VTKGLNP   MKDS +EW+G 
Sbjct: 173 SKIFEFLDHETAKIDSLIKKQQQLIKLLKEKRQAVISHAVTKGLNPQAPMKDSDVEWLGK 232

Query: 228 VPDHWEVKPFFALVTELNR--KNTKLIES-------NILSLSYGNIIQKLETRNMGLKPE 278
           VP+HW     F + T +     +T L E        N  +L+ G I      + + LK  
Sbjct: 233 VPEHWGTPKLFHVSTRIGDGLHSTPLYEDGTGYFFVNGNNLTNGVITIGATAKEVPLK-- 290

Query: 279 SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMR 338
            Y+ + I      V   I+      +L   + +  G  ++AY+  K   I+  YL W + 
Sbjct: 291 EYQNHYIPLSNMSVLLSINGTIGNVALYREEKIILG-KSAAYINCKAE-INPEYLRWFLT 348

Query: 339 SYDLCKVFYAM---GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           S D  K++Y +   G+ +  +L    ++++ VLVP ++EQ DI     +  ++ + L+  
Sbjct: 349 S-DQAKLYYDLEVTGTTIY-NLSLNSIRKMKVLVPSVQEQTDIAKFCEMSHSKYEKLILS 406

Query: 396 IEQSIVLLKERRSSFIAAAVTGQIDLRG 423
               + LLKERR++ I+AAVTG+ID+R 
Sbjct: 407 AITQMDLLKERRTALISAAVTGKIDVRN 434


>gi|260578144|ref|ZP_05846064.1| restriction modification system DNA specificity domain protein
           [Corynebacterium jeikeium ATCC 43734]
 gi|258603683|gb|EEW16940.1| restriction modification system DNA specificity domain protein
           [Corynebacterium jeikeium ATCC 43734]
          Length = 383

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 107/330 (32%), Positives = 178/330 (53%), Gaps = 18/330 (5%)

Query: 103 FDGICSTQFLVLQPKDVLPELLQG----WLLSIDVTQRIEAICEGATMSHADWKGIG--- 155
           FDG+ S  + V + +++  E + G    ++  +  ++ I         +   W+      
Sbjct: 53  FDGLTSPDYRVFRARNL--EFINGRYFLYVFQLLYSRHIYYKFGQGVSNMGRWRLPADVF 110

Query: 156 -NIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPD 214
            N P+P+PP  EQ  I   +  +T  ID LI +     ELL+  ++ L++  VT+GL+PD
Sbjct: 111 LNFPLPVPPRLEQAEISNYLDEKTAEIDGLIGKLGHQAELLERYRRELIARTVTRGLDPD 170

Query: 215 VKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQK----LET 270
             M+DSGI+W G +P  W  +PF AL +   + N+ L   N L    G I+ K     E 
Sbjct: 171 APMRDSGIDWAGDMPKTWRTQPFVALFSVEKKINSDLRIRNALQFRNGEIVVKPGWYPED 230

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH-GID 329
           R +    E+  TY++V PG IV   ++L  D R+ R   V + G+ITSAY+ +  + GID
Sbjct: 231 RKLD---ETLATYKVVTPGMIVINGLNLNYDFRTKRIGLVTQNGVITSAYITLSANLGID 287

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
             + ++L++S D   +F+ M  G+R+ L + D++R  + VPP++EQ +I + +  ++A I
Sbjct: 288 ERFASYLLKSMDSRLLFHGMAEGVRKILSWADIRREKIPVPPLREQTEIADFLEEKSAEI 347

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           D  +E I++ I LL + R   I  AVTG+I
Sbjct: 348 DTTIEGIKRQIELLGKYRKQVINDAVTGKI 377



 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 76/172 (44%), Gaps = 11/172 (6%)

Query: 256 ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGI 315
           ILS++   I  K   +N G    +Y+ YQ+V+ G+     +DL          Q    G+
Sbjct: 1   ILSITQSGIKPKNILQNEGQMARNYDGYQVVNQGDFAMNSMDLLTGWVD----QSPFDGL 56

Query: 316 ITSAYMAVKPHG---IDSTYLAWLMRSYDLCKVFYAMGSGL----RQSLKFEDVKRLPVL 368
            +  Y   +      I+  Y  ++ +      ++Y  G G+    R  L  +     P+ 
Sbjct: 57  TSPDYRVFRARNLEFINGRYFLYVFQLLYSRHIYYKFGQGVSNMGRWRLPADVFLNFPLP 116

Query: 369 VPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           VPP  EQ +I+N ++ +TA ID L+ K+     LL+  R   IA  VT  +D
Sbjct: 117 VPPRLEQAEISNYLDEKTAEIDGLIGKLGHQAELLERYRRELIARTVTRGLD 168



 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 49/204 (24%), Positives = 91/204 (44%), Gaps = 9/204 (4%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESG-KDIIYIGLEDVESGTGKYLPKDGN 69
           +DSG+ W G +PK W+  P      +     S+   ++ +     ++    G Y P+D  
Sbjct: 174 RDSGIDWAGDMPKTWRTQPFVALFSVEKKINSDLRIRNALQFRNGEIVVKPGWY-PEDRK 232

Query: 70  SRQSDTSTVSIFAKGQILYGKLG---PYLRKAI-IADFDGICSTQFLVLQPKDVLPELLQ 125
             ++  +T  +   G I+   L     +  K I +   +G+ ++ ++ L     + E   
Sbjct: 233 LDET-LATYKVVTPGMIVINGLNLNYDFRTKRIGLVTQNGVITSAYITLSANLGIDERFA 291

Query: 126 GWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
            +LL S+D       + EG     + W  I    +P+PPL EQ  I + +  ++  IDT 
Sbjct: 292 SYLLKSMDSRLLFHGMAEGVRKILS-WADIRREKIPVPPLREQTEIADFLEEKSAEIDTT 350

Query: 185 ITERIRFIELLKEKKQALVSYIVT 208
           I    R IELL + ++ +++  VT
Sbjct: 351 IEGIKRQIELLGKYRKQVINDAVT 374


>gi|332664152|ref|YP_004446940.1| restriction modification system DNA specificity domain-containing
           protein [Haliscomenobacter hydrossis DSM 1100]
 gi|332332966|gb|AEE50067.1| restriction modification system DNA specificity domain protein
           [Haliscomenobacter hydrossis DSM 1100]
          Length = 417

 Score =  173 bits (439), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 131/393 (33%), Positives = 205/393 (52%), Gaps = 27/393 (6%)

Query: 50  YIGLEDVESGTGKYL--PKDGNS-----RQSDTSTVSIFAKGQILYGKLGPYLRKAIIAD 102
           YIGLE +ES +G+ L  P +         ++  S  ++F  G +L+GKL PYL KA +A+
Sbjct: 29  YIGLEHIESSSGRLLISPLENGDLPDEMAEAGESLCNLFEPGDVLFGKLRPYLAKAWVAN 88

Query: 103 FDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
           F G C+T+ +VL PK + P  L+   L  ++   I     G+ M  ADW  IG+  +  P
Sbjct: 89  FSGRCTTELIVLIPKLIDPYYLKYNFLEKELLDAITGSSFGSKMPRADWGFIGDQYIFFP 148

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
           P+  Q  I   +  ET RID LI+ + R I LL EK+QAL++  VT+G + ++KMK +G+
Sbjct: 149 PIDIQRRIASYLDRETTRIDGLISAKERLITLLAEKRQALITQAVTRGFDQEIKMKHAGV 208

Query: 223 EWVGLVPDHW-EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK----- 276
           EW+G VPD W E++  +               ++ L L     + + E R  GL      
Sbjct: 209 EWIGEVPDGWMEIRVKYLGDIFYGLSQPPGYHADGLPLVRATNVYRGEIRKEGLVFVNED 268

Query: 277 --PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME--RGIITSAYMAVKPHG-IDST 331
             PES +   I+  G+I+     +++   +  SA V E   G +    M  KP+  ++  
Sbjct: 269 DLPESKKV--ILKTGDIII----VRSGAYTADSALVTEEWEGAVAGFDMVFKPNKRVNPN 322

Query: 332 YLAWLMRS-YDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPP-IKEQFDITNVINVETAR 388
           +LA+++ S Y L      M     Q  L  E++    V++PP + EQF I   +  + ++
Sbjct: 323 FLAYVLLSPYVLESQLIPMSVRAAQPHLNAEELGSTIVVLPPSVDEQFAIIQCLEKKISK 382

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           +D L     +SI LLKERR + I+AAVTGQI++
Sbjct: 383 LDALRVANTKSIELLKERRKALISAAVTGQIEI 415



 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 53/209 (25%), Positives = 96/209 (45%), Gaps = 9/209 (4%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           + K +GV+WIG +P  W  + +K    +  G +   G     + L    +     + K+G
Sbjct: 202 KMKHAGVEWIGEVPDGWMEIRVKYLGDIFYGLSQPPGYHADGLPLVRATNVYRGEIRKEG 261

Query: 69  ----NSRQSDTSTVSIFAKGQILYGKLGPYLRKA--IIADFDGICSTQFLVLQP-KDVLP 121
               N      S   I   G I+  + G Y   +  +  +++G  +   +V +P K V P
Sbjct: 262 LVFVNEDDLPESKKVILKTGDIIIVRSGAYTADSALVTEEWEGAVAGFDMVFKPNKRVNP 321

Query: 122 ELLQGWLLSIDVTQ-RIEAICEGATMSHADWKGIGNIPMPIPP-LAEQVLIREKIIAETV 179
             L   LLS  V + ++  +   A   H + + +G+  + +PP + EQ  I + +  +  
Sbjct: 322 NFLAYVLLSPYVLESQLIPMSVRAAQPHLNAEELGSTIVVLPPSVDEQFAIIQCLEKKIS 381

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVT 208
           ++D L     + IELLKE+++AL+S  VT
Sbjct: 382 KLDALRVANTKSIELLKERRKALISAAVT 410


>gi|282901858|ref|ZP_06309764.1| Restriction modification system DNA specificity domain protein
           [Cylindrospermopsis raciborskii CS-505]
 gi|281193254|gb|EFA68245.1| Restriction modification system DNA specificity domain protein
           [Cylindrospermopsis raciborskii CS-505]
          Length = 445

 Score =  173 bits (438), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 140/444 (31%), Positives = 218/444 (49%), Gaps = 35/444 (7%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGKDIIYIG------- 52
           +K +K YP YKDSGV+W+G IP+HW+V  +   F K+ +G T  +     Y G       
Sbjct: 13  VKGWKRYPAYKDSGVEWLGKIPEHWEVRKVSHAFQKIGSGTTPSTNHYDYYEGNIPWVNT 72

Query: 53  ---LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
               E V + T   L    N    D S ++++  G +L    G  + +  I      C+ 
Sbjct: 73  SELREKVITDTSAKL---TNKALLDHSVLNLYPPGTLLIAMYGATIGRLGILGITA-CTN 128

Query: 110 QFL--VLQPKDVLPELLQGWLLSIDVTQRIEAI--CEGATMSHADWKGIGNIPMPIPPLA 165
           Q    +  P  +  +    WL      +R E I    G    + + + I +I +P PPL 
Sbjct: 129 QACCALANPISINAKFAFYWLW----MRRNELILLSSGGGQPNINQEKIRSIRIPAPPLT 184

Query: 166 EQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           EQ  I + +  ET +IDTL+ ++ R IELLKEK+ AL+S+ VTKGLNPD  MKDSG+EW+
Sbjct: 185 EQQAIAQFLDRETAKIDTLVAKKERLIELLKEKRTALISHAVTKGLNPDAPMKDSGVEWL 244

Query: 226 GLVPDHWEVKPFFALVTELNRKNTKLIE--SNILSLSYGNIIQKLETRNMGLKPESYE-T 282
           G VP +W   P   L       + KL +   N+  +   +I  K     +    E+ E T
Sbjct: 245 GEVPRNW---PMIRLKHVAPVSSAKLTQKPDNLPYIGLEHIESKTGRLLLDTPVENVEST 301

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYD 341
               + G+++F  +     K  L   +    G+ T+  +A+KP   ++  +L + + +  
Sbjct: 302 VSCFEKGDVLFGKLRPYLAKVLLAEFE----GVSTTELLALKPSQDVNGKFLFFQLIAEG 357

Query: 342 LCKVFYAMGSGLRQS-LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
                 +   G +   +  E +  L + +PP+ EQ  I   ++ ETA+ID LV K   SI
Sbjct: 358 FIDQVNSFTYGTKMPRVGPEQITNLFIPLPPLPEQQAIAQFLDRETAKIDTLVAKTRTSI 417

Query: 401 VLLKERRSSFIAAAVTGQIDLRGE 424
             LKE R++ I+AAVTG+ID+R E
Sbjct: 418 EKLKEYRTALISAAVTGKIDVREE 441



 Score = 68.2 bits (165), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 105/235 (44%), Gaps = 36/235 (15%)

Query: 207 VTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI-- 264
           + KG       KDSG+EW+G +P+HWEV+       ++    T    +N      GNI  
Sbjct: 12  IVKGWKRYPAYKDSGVEWLGKIPEHWEVRKVSHAFQKIGSGTTP--STNHYDYYEGNIPW 69

Query: 265 IQKLETRNMGLKPES----------YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERG 314
           +   E R   +   S          +    +  PG ++           ++  A +   G
Sbjct: 70  VNTSELREKVITDTSAKLTNKALLDHSVLNLYPPGTLLI----------AMYGATIGRLG 119

Query: 315 II-------TSAYMAVKPHGIDSTY-LAWL-MRSYDLCKVFYAMGSGLRQSLKFEDVKRL 365
           I+        +      P  I++ +   WL MR  +L  +  + G G + ++  E ++ +
Sbjct: 120 ILGITACTNQACCALANPISINAKFAFYWLWMRRNEL--ILLSSGGG-QPNINQEKIRSI 176

Query: 366 PVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            +  PP+ EQ  I   ++ ETA+ID LV K E+ I LLKE+R++ I+ AVT  ++
Sbjct: 177 RIPAPPLTEQQAIAQFLDRETAKIDTLVAKKERLIELLKEKRTALISHAVTKGLN 231


>gi|77166146|ref|YP_344671.1| restriction endonuclease S subunits-like [Nitrosococcus oceani ATCC
           19707]
 gi|254435813|ref|ZP_05049320.1| hypothetical protein NOC27_2876 [Nitrosococcus oceani AFC27]
 gi|76884460|gb|ABA59141.1| Restriction endonuclease S subunits-like protein [Nitrosococcus
           oceani ATCC 19707]
 gi|207088924|gb|EDZ66196.1| hypothetical protein NOC27_2876 [Nitrosococcus oceani AFC27]
          Length = 487

 Score =  172 bits (435), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 143/447 (31%), Positives = 225/447 (50%), Gaps = 37/447 (8%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +YK+S V WIG +P  W+V P K     N G     G D    G   V   T + +  
Sbjct: 31  YREYKNSDVVWIGEVPSFWEVKPFKWLLTHNEGGVW--GDDPAGEGDTIVLRSTDQTV-- 86

Query: 67  DGNSRQSDTS----TVSIFAKGQILYGKL--------GPYLRKAIIADFD----GICSTQ 110
           DGN   +D +    TV   A   +  G L          ++ K  + + D    G C   
Sbjct: 87  DGNWNVTDPAVRHLTVKENASAVLEAGDLVVTKSSGSALHIGKTTLVNVDMAKLGYCYGN 146

Query: 111 FL--VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAE 166
           F+  +   +  +P+L   ++++ D+ +    +   +T   A+     IG I +P+PP+ E
Sbjct: 147 FMQRLRLGQKYIPKLAW-YVMNNDLVRLQLNLLSNSTTGLANLNATLIGEILLPVPPVEE 205

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q  I   +  ET RID LI E+ R IELLKEK+QA++S+ VTKGL+P V MKDSG+EW+G
Sbjct: 206 QTQIARFLDHETARIDALIEEQQRLIELLKEKRQAIISHAVTKGLDPTVPMKDSGVEWLG 265

Query: 227 LVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY-----E 281
            VP HW  KP   L  ELN K +     +   L     ++KL+T  + L  E +      
Sbjct: 266 EVPAHWITKPLKHLA-ELNPKKSGY-HGDRDELCSFVPMEKLKTGVIQLDEERFIADVIS 323

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGI--ITSAYMAVKPH-GIDSTYLAWLMR 338
            Y   + G+++   +    + R++  A  +  G+   +S    ++P   +++++L + ++
Sbjct: 324 GYTYFEDGDVLQAKVTPCFENRNIAIADGLTNGVGFGSSEINVLRPFPDVNASFLYYRLQ 383

Query: 339 SYDLCKVFYA--MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
                 +  A  +G+G  + +  E +    V VP   EQ  I + ++ ETAR+D LVE+ 
Sbjct: 384 EDGYMGICTASMIGAGGLKRVPGEVINGFTVAVPERHEQTQIAHFLDHETARVDKLVEEA 443

Query: 397 EQSIVLLKERRSSFIAAAVTGQIDLRG 423
              I LLKERRS+ I+AAVTG+ID+RG
Sbjct: 444 NVGIELLKERRSALISAAVTGKIDVRG 470


>gi|288928859|ref|ZP_06422705.1| probable type I restriction-modification system [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288329843|gb|EFC68428.1| probable type I restriction-modification system [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 428

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 125/428 (29%), Positives = 213/428 (49%), Gaps = 30/428 (7%)

Query: 10  YKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           YKDSGV+W+G IP+HW+V  IK  FT+      S+ G        E +   T KY     
Sbjct: 13  YKDSGVKWLGNIPQHWEVRKIKYVFTE-----RSQKG-----FPKEPILCSTQKYGVIPQ 62

Query: 69  NSRQSDTSTVSIFAKGQILYGK------LGPYLRKAIIADFDGICSTQFLVLQPKD-VLP 121
           +  ++    V+   +G  L  K      L  +      A + GI S  + +L   D    
Sbjct: 63  HMYENRVVVVNKGLEGLKLVRKGDFVISLRSFQGGIEYAYYQGIISAAYTILNLNDNCYS 122

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMS-HADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
             ++  + S D  Q ++    G     + ++  +    +P+PPLAEQ  I   +  +  +
Sbjct: 123 NYIKYLMKSFDFIQLLQTCVTGIREGQNINYTLLRKSSLPLPPLAEQRAIVSYLDGKVGQ 182

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           IDT + ++ + IELLKE KQA+++  VTKG++   K+K +GI W+G VP HWE      +
Sbjct: 183 IDTYVAKQTQQIELLKELKQAVIANAVTKGIDNKAKLKQTGISWIGHVPQHWERCRCKDV 242

Query: 241 VTELNRKNTKLIESN----ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFI 296
           +TE+     KL+  N    +LSL+   +I +  +   G  P+ + TY++V P ++VF   
Sbjct: 243 LTEI-----KLLVGNGEYALLSLTTNGVIVRDLSEGKGKFPKDFNTYKVVKPNDLVFCLF 297

Query: 297 DLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQS 356
           D+    R++    V   G++T AY   +   +D+++L     + D  K    +  GLR+ 
Sbjct: 298 DVDETPRTV--GLVHNHGMLTGAYNVFETKNVDTSFLYHYFIALDNRKALKPLYKGLRKV 355

Query: 357 LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           +       +P+ +PP+ EQ  I + I  +TA I+ L++  EQ +  +KE +   I+ AVT
Sbjct: 356 IPLPAFMSMPLYIPPLSEQRAIVSYIEAKTASINKLIDAYEQQVERVKEYKQRLISDAVT 415

Query: 417 GQIDLRGE 424
           G++++  E
Sbjct: 416 GKMNVTDE 423


>gi|255320275|ref|ZP_05361460.1| restriction endonuclease S subunit [Acinetobacter radioresistens
           SK82]
 gi|255302714|gb|EET81946.1| restriction endonuclease S subunit [Acinetobacter radioresistens
           SK82]
          Length = 461

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 141/467 (30%), Positives = 229/467 (49%), Gaps = 65/467 (13%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES------GKDIIYIGLE 54
           M  Y+AY +YKDSGV+W+G +P HW +  +KR+  +  G    S      G  +I IG  
Sbjct: 1   MAKYQAYAEYKDSGVEWLGVVPSHWIITTLKRYCYVKGGFAFSSDAFIDTGYPVIRIG-- 58

Query: 55  DVESG------TGKYLPKD--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGI 106
           D+++         KY+P+    NSR        +  K Q+L    G  + KA +      
Sbjct: 59  DIKTDGSINLENCKYIPESLAVNSRDY------LVEKNQLLMAMTGATIGKAGL-----Y 107

Query: 107 CSTQFLVLQPKDVLPELLQG--------WLLSIDVTQR-IEAICEGATMSHADWKGIGNI 157
            S Q   L  +    ELL          ++L  D  Q  I+    G    +     + + 
Sbjct: 108 TSNQPAFLNQRVGKFELLAQNMNYRYLWYILKTDGYQEYIKLTAFGGAQPNISDTAMVDY 167

Query: 158 PMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKM 217
           P  IP   EQ  I   +  ET +ID LI ++ R IELLKEK+QA++S+ VTKGLNP+V M
Sbjct: 168 PATIPSFDEQTQIANFLDHETSKIDHLIEKQQRLIELLKEKRQAVISHAVTKGLNPNVPM 227

Query: 218 KDSGIEWVGLVPDHWEVK------PFFALVTELNRKNTKLIESN--ILSLSYGNIIQKLE 269
           KDSG+EW+G VP+HW +         F  +         +++ +   L LS  NI     
Sbjct: 228 KDSGVEWLGEVPEHWRISRLKYNASIFGRIGFRGYTVDDIVDEDEGALVLSPSNISN--- 284

Query: 270 TRNMGLKPESYETYQ--------IVDPGEIVFRFIDLQNDKRSLRSAQV---MERGIITS 318
              + L+ ++Y +++        IVD  +++     ++      +SA +   +E   I  
Sbjct: 285 ANKLTLEKKTYLSWKKYFESPEIIVDENDLLL----VKTGSTFGKSAIIVNKLEPMTINP 340

Query: 319 AYMAVKPHGIDSTYLAWLMRSYDLCKVF--YAMGSGLRQSLKFEDVKRLPVLVPPIKEQF 376
               +K   I+  +L +L  S  +  +      GSG+  ++  E++   P+ +P  +E  
Sbjct: 341 QMALIKKSKIEPRFLGYLFGSKLIKSIIENSNTGSGM-PTMTQENINNFPIPLPSDEEAI 399

Query: 377 DITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            I+N ++ +T +ID L+EK EQ+I+L++ERR++ I+AAVTG+ID+R 
Sbjct: 400 IISNYLDNKTYKIDFLIEKSEQTILLMQERRTALISAAVTGKIDVRN 446


>gi|299068119|emb|CBJ39334.1| putative type I restriction-modification methylase S subunit
           [Ralstonia solanacearum CMR15]
          Length = 445

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 142/440 (32%), Positives = 207/440 (47%), Gaps = 28/440 (6%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M HYK YP YKDSGV+W+G +P HW V  +         R   S KD   + +  +    
Sbjct: 1   MSHYKPYPAYKDSGVRWLGKVPAHWSVGRLA--NSFEERRAKVSDKDFPALSVTKL---- 54

Query: 61  GKYLPKDGN-SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-D 118
              +P+  N ++  D     +  KG I           + +AD DG  S    VL PK  
Sbjct: 55  -GVVPQLENVAKTDDGDNRRMVLKGDIAINSRSDRKGASGLADRDGSVSLIITVLTPKPS 113

Query: 119 VLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
           V  E     + S    +    +  G  A +   ++  +  I +  PP+ EQ  I   +  
Sbjct: 114 VWGEYCHHLIRSEIFQEEYFRVGNGLVADLWTTNYSSMRTIFLARPPIEEQKAIASHLDR 173

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK- 235
           ET RID L+ ++ RFIELL EK+QAL+++ VTKGL P   MK SG+EW+G VP+HW +K 
Sbjct: 174 ETARIDALVEKKTRFIELLGEKRQALITHAVTKGLGPGKPMKGSGVEWLGEVPEHWVIKR 233

Query: 236 -PFFALVTELNRKNTKLIESNILSLSY---GNIIQKL----ETRNMGLKPESYETYQIVD 287
             F A V     K   L + + + + Y    N+        E   + +     E Y ++ 
Sbjct: 234 LKFIARVQTGVAKGKDLADKDTIEVPYLRVANVQDGFLDLDEVATIEIDKRDLERY-LLQ 292

Query: 288 PGEIVFR-FIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVF 346
            G+++     D     R    +  +   I  +   AV+PHG+ S +L     S      F
Sbjct: 293 LGDVLMNEGGDFDKLGRGHVWSGEISPCIHQNHVFAVRPHGVSSPWLNAFTSS--AAAQF 350

Query: 347 YAMGSGLRQ----SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
           Y MG   +     S+   ++  LPV VPP  EQF+I   +     ++D +V K E+SI L
Sbjct: 351 YFMGKSKQSTNLASISSSNLMELPVPVPPEPEQFEILAEVQKNLEKLDNVVRKTERSIEL 410

Query: 403 LKERRSSFIAAAVTGQIDLR 422
           L+E RS+ I AAVTGQIDLR
Sbjct: 411 LREHRSALITAAVTGQIDLR 430


>gi|152984823|ref|YP_001345472.1| type I restriction-modification system subunit S [Pseudomonas
           aeruginosa PA7]
 gi|150959981|gb|ABR82006.1| type I restriction-modification system, S subunit [Pseudomonas
           aeruginosa PA7]
          Length = 464

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 127/456 (27%), Positives = 217/456 (47%), Gaps = 48/456 (10%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIK-----RFTKLNTGRTSESGKDIIYIGLEDVES 58
           +  YP+Y+ SGV+W+  +P HW  VPIK     R +    G   ES KDI   G+  + +
Sbjct: 3   FPCYPKYRASGVEWLDQVPDHWSSVPIKYMALERNSLFLDGDWIES-KDISSDGIRYITT 61

Query: 59  GT---GKYLPKDGNSRQSDTST---VSIFAKGQILYGKLG-PYLRKAIIADFDG--ICST 109
           G    G Y  +       +T      +   +G +L  +L  P  R  ++ +  G  + S 
Sbjct: 62  GNVGEGAYKEQGAGFISEETFHALRCTEVYEGDVLVSRLNNPIGRACVVPNLGGRVVTSV 121

Query: 110 QFLVLQPKDVLPELLQGWLLSID-VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
             ++ +P     +    +L S +   +    +  GATM       +GNI +  P L EQ 
Sbjct: 122 DNVIFRPDLKFYKKFIVYLFSSEEYFKHTSNLARGATMQRISRGLLGNIRVVTPSLEEQT 181

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I   +  ET RID LI E+ R IELLKEK+QA++S+ VTKGL+P V MKDSG+EW+G V
Sbjct: 182 QIARFLDHETARIDALIEEQQRLIELLKEKRQAVISHAVTKGLDPTVPMKDSGVEWLGEV 241

Query: 229 PDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPE---------- 278
           P HWEV+   ++  ++           ++       +Q L  ++  +K E          
Sbjct: 242 PAHWEVRSISSISKKITNGYVGPTRDILVDEPGVRYLQSLHIKSNKIKFEVPYFVSEQWS 301

Query: 279 SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG----------I 328
           +     I+  G+++            +++  + +  ++T  +     H           +
Sbjct: 302 AEHAKSILASGDVLI-----------VQTGDIGQVAVVTEEHAGCNCHALIIVSPVREVV 350

Query: 329 DSTYLAWLMRS-YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETA 387
              +++W++ S Y    +       +   L   +VK L + +PP++EQ  I + I     
Sbjct: 351 LGEWVSWVLNSTYGYHSLLSIQTGAMHPHLNCGNVKFLNLPIPPLEEQARIVSFIESGEL 410

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            +D L+ + ++S++LL+ERR++ I+AAVTG+ID+RG
Sbjct: 411 EMDSLMSETKRSLLLLQERRTALISAAVTGKIDVRG 446


>gi|307720089|ref|YP_003891229.1| Restriction endonuclease S subunit [Sulfurimonas autotrophica DSM
           16294]
 gi|306978182|gb|ADN08217.1| Restriction endonuclease S subunit [Sulfurimonas autotrophica DSM
           16294]
          Length = 442

 Score =  170 bits (431), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 128/443 (28%), Positives = 205/443 (46%), Gaps = 32/443 (7%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGK 62
           YK YP YKDSG+ W+G +P  W V  +K   +    + S    KDI+ + +     G   
Sbjct: 5   YKPYPSYKDSGIAWLGEVPIGWDVRRLKTILQERREKNSPVKTKDILSLCMY---RGVIP 61

Query: 63  YLPK--DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           Y  K   GN  + D +   +     I+   +        ++ + G  S  + +L P+   
Sbjct: 62  YSEKGNSGNKAKDDLTAYKLAYPNDIVLNSMNVVAGSVGLSKYFGAVSPVYYMLYPRKST 121

Query: 121 PEL--LQGWLLSIDVTQRIEAICEGATMSHADWKG-------------IGNIPMPIPPLA 165
            ++        S    + +  +  G  +  ++  G             + ++ MPIPP  
Sbjct: 122 DDISYFNAIFQSESFQKSLIGLGNGILVKQSEKTGKLNTIRMKISMDSLNDVLMPIPPFQ 181

Query: 166 EQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           EQ  I   +   T +IDTLI ++ + I LLKEK+QA++S  VT+GL+  V MKDSG+EW+
Sbjct: 182 EQQTIANYLDNATAKIDTLIEKQTKLIALLKEKRQAVISTAVTRGLDSSVPMKDSGVEWL 241

Query: 226 GLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQI 285
           G +P+HWEVK F  L  E+ ++ +  +  +ILS++   I  K      G     Y  YQ 
Sbjct: 242 GEIPEHWEVKKFKYLF-EIRKRISGKLGYDILSITQKGIKVKDIESGKGQLSSDYSKYQH 300

Query: 286 VDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY--MAVKPHGIDSTYLAWLMRSYDLC 343
           V  G+     +DL      L        G+ +  Y   ++     D+ Y  +L++   + 
Sbjct: 301 VYKGDYAMNHMDLLTGFVDLSKYD----GVTSPDYRVFSIIEKNADANYYLFLLQMGYIN 356

Query: 344 KVFYAMGSGLRQ----SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           K+FY +G G  Q     L  +  K      PP +EQ  I   I+    +   L  K  ++
Sbjct: 357 KIFYPLGQGSSQFGRWRLPSDAFKEFQAPFPPQEEQKKIAKYIDDSLTKFTKLTTKATKA 416

Query: 400 IVLLKERRSSFIAAAVTGQIDLR 422
           I LLKERR++ I+A VTG+ID+R
Sbjct: 417 IELLKERRTALISAIVTGKIDVR 439


>gi|300113140|ref|YP_003759715.1| restriction modification system DNA specificity domain-containing
           protein [Nitrosococcus watsonii C-113]
 gi|299539077|gb|ADJ27394.1| restriction modification system DNA specificity domain protein
           [Nitrosococcus watsonii C-113]
          Length = 482

 Score =  169 bits (429), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 136/454 (29%), Positives = 214/454 (47%), Gaps = 50/454 (11%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT---SESGKDIIYIGLEDVESGT 60
           +  YP YKDSGV+W+G +P+HW    +K F +LN  ++    + G+   +I +E +++G 
Sbjct: 28  FPRYPAYKDSGVEWLGEVPEHWTTTSLKYFAELNPKKSDYRGDQGQLCSFIPMEKLKTGA 87

Query: 61  GKYLPKDGNSRQSDTST-VSIFAKGQILYGKLGPYLRKAIIADFDGIC------STQFLV 113
              +  D     +D  T  + F  G +L  K+ P      IA  DG+       S++  V
Sbjct: 88  ---IQLDEVRTIADVITGYTYFEDGDVLQAKVTPCFENGNIAIADGLTNGVGFGSSEINV 144

Query: 114 LQPKDV-----LPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
           ++P  +        L +G  +SI     I A      +     + I    + IP   EQ 
Sbjct: 145 IRPFKIDVGFLYYRLQEGVFMSICTASMIGA----GGLKRVPGEVIDGFTVAIPDRNEQT 200

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I   +  ET RID LI E+ R IELLKEK+QA++S+ VTKGL+P V MKDSG+EW+G V
Sbjct: 201 QIARFLDHETARIDALIAEQQRLIELLKEKRQAVISHAVTKGLDPTVPMKDSGVEWLGEV 260

Query: 229 PDHWEVKP---FFALVTELNRKNTKLIESNILSLSYGNIIQ-KLETRNMGLKPESYETYQ 284
           P HWEVK    +  ++     K+T   +   L +   N+     E  +    PES+    
Sbjct: 261 PAHWEVKKIKHYGRVIGGFAFKSTDFSDEGHLVIKISNVGHLGFEWNDASYLPESFTVRH 320

Query: 285 ---IVDPGEIVF-----------RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDS 330
              I   G ++F           +   L+ D R L + +V         ++++    + S
Sbjct: 321 SEFIAPKGSLIFAMTRPVISGGIKIARLEKDLRPLINQRV--------GFISINDEAL-S 371

Query: 331 TYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
            YL    +S      F    +   Q ++  E ++ + + +PP +E   I   I     + 
Sbjct: 372 RYLLVSSQSESFLSQFKNNLTITNQPNIASEGIESISIPIPPAEELRRILEYIETLIDKF 431

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           D L+      I LL+ERRS+ I+AAVTG+ID+RG
Sbjct: 432 DCLMLDACSGIRLLQERRSALISAAVTGKIDVRG 465


>gi|188585426|ref|YP_001916971.1| restriction modification system DNA specificity domain
           [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|179350113|gb|ACB84383.1| restriction modification system DNA specificity domain
           [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 441

 Score =  169 bits (428), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 130/447 (29%), Positives = 229/447 (51%), Gaps = 44/447 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKL---NTGRTSESGKDIIYIGLEDVE 57
           M+ +K Y +YKDSG++W+G +P HW +  +  +TK    +  R +  GK + Y  +  +E
Sbjct: 1   MEKFKQYKKYKDSGIEWLGKVPSHWDINRMDAYTKYYKKSIEREALRGKTVFYYSIPAIE 60

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII-----ADFDGICSTQFL 112
             TG  + ++G++  S+   +        L  KL P  RK  I      +   ICS++F+
Sbjct: 61  E-TGDGVVEEGSNIDSNKLLLKGEEL---LVSKLNP--RKGRIIPTKEKEMPIICSSEFV 114

Query: 113 VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSH--ADWKGIGNIPMPIPPLAEQVLI 170
            L P++   E ++    S  V Q++ +  + AT SH   + + I  I    P  +EQ  I
Sbjct: 115 PLVPRNCSREFIRYIYQSELVKQKLSSAVQSATNSHQRVNPRDISKIYFAFPSKSEQDNI 174

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
            + + ++T +ID+LI ++   IE L+E KQ+L+++ VTKGL+P+VKMKDSG+EW+G VP+
Sbjct: 175 VKYLNSKTSQIDSLINKKQNLIEKLQEYKQSLITHTVTKGLDPNVKMKDSGVEWIGEVPE 234

Query: 231 HWEVKPFFALVTELN-----------RKNTKLIESNILSLSYGNII---QKLETRNMGLK 276
           HWE+     L+   N               K I+ + L+     ++    KL+ +N   +
Sbjct: 235 HWEILKGKYLLDIYNGYPPEELSLSANGQVKYIQVDDLNTENDELVIKDSKLKLKNKKTE 294

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAW 335
              +    I   G  +F          + +   ++++G+I S  M +KP    +  YL +
Sbjct: 295 ALDHPIILIPKRGAAIF----------TNKVKILVDKGLIDSNIMGLKPKKNCNIHYLVY 344

Query: 336 LMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           ++++  +  +  A  S + Q +  + +  LP+ +PPI+EQ  I   ++ +   I+  +  
Sbjct: 345 MIKARKVDDI--ADTSTIPQ-INNKHINPLPLTIPPIEEQNKIAEYLDEKVDNINNCILN 401

Query: 396 IEQSIVLLKERRSSFIAAAVTGQIDLR 422
           I+ +I  LKE R S I  AVTG+ID+R
Sbjct: 402 IKVAIQKLKEYRQSLITHAVTGKIDVR 428


>gi|218960560|ref|YP_001740335.1| putative Type I restriction-modification system specificity subunit
           [Candidatus Cloacamonas acidaminovorans]
 gi|167729217|emb|CAO80128.1| putative Type I restriction-modification system specificity subunit
           [Candidatus Cloacamonas acidaminovorans]
          Length = 440

 Score =  169 bits (427), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 141/463 (30%), Positives = 216/463 (46%), Gaps = 67/463 (14%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKL--NTGRTSESGKDIIY-IGLEDV- 56
           M  YK+Y  YK++G+ W+  +PKHW+++     T    N     E   + ++   +  V 
Sbjct: 1   MIKYKSYEDYKETGITWLTMVPKHWEILRTDSVTVYIRNQINPDEIKSEFVFHYSIPAVQ 60

Query: 57  ESGTGKY--LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA-----DFDGICST 109
           E+GTG+Y    + G+++Q       +  K  +L  KL P  RKA I      D   ICS+
Sbjct: 61  ETGTGQYDLTEEVGSAKQ-------LITKKSVLISKLNP--RKATICIAEPKDEITICSS 111

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADW--KGIGNIPMPIPPLAEQ 167
           +F+ ++ K    + L   + S    QR++A  +  T SH       I      +P   EQ
Sbjct: 112 EFIAMEAKKCDLKYLFYLMNSEMNRQRLDAKVQSVTRSHQRVYPSDIYRFWTALPSTTEQ 171

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I   +  ET RID LI ++ R IELLKEK+ AL++  VTKGL+P+V MKDSGIEW+G 
Sbjct: 172 QAIASFLDRETARIDALIQKKERMIELLKEKRIALITQAVTKGLDPNVPMKDSGIEWLGE 231

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
           VP+HW V  F                 NI S   G      E    GL+ E    Y++ D
Sbjct: 232 VPEHWTVLKF----------------KNIGSFQGGAGFPDDE---QGLEDEEIPFYKVSD 272

Query: 288 ---PGEIVFRFIDLQNDKRS----LRSAQVMERGIITSAYMAV----------KPHGIDS 330
              PG   +      +  R     LR++ + +  I+ +   A           K   ID+
Sbjct: 273 MNLPGNETYMCQHNNSVSRETALKLRASILRKNTIVFAKVGAALLLNRRRIITKDSCIDN 332

Query: 331 TYLAWLMRSYDLCKVFYAM---------GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNV 381
             + +     D+   ++ +           G   S+    +  +PV VPP +EQ  I + 
Sbjct: 333 NMMGFSTTHCDVMWCYFFLFQLDLGKLVNPGAVPSVNESQMSNIPVCVPPTQEQKQIGDY 392

Query: 382 INVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           +  ET +I+ +++K+  SI+ L E R+S I  AVTG+IDLRG 
Sbjct: 393 LVTETTKINKMIDKVNASIIQLSEYRASLIHHAVTGKIDLRGH 435


>gi|330992551|ref|ZP_08316499.1| hypothetical protein SXCC_02458 [Gluconacetobacter sp. SXCC-1]
 gi|329760750|gb|EGG77246.1| hypothetical protein SXCC_02458 [Gluconacetobacter sp. SXCC-1]
          Length = 432

 Score =  169 bits (427), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 132/443 (29%), Positives = 219/443 (49%), Gaps = 37/443 (8%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES------GKDIIYI-GLEDV 56
           +  YP YKDSGV+WIG IP  W    +K    ++ G++  S      G  + ++ G  D 
Sbjct: 3   FPKYPAYKDSGVEWIGEIPVGWHSACLKHVAIVDAGQSPASTDCNTEGCGLPFLQGCADF 62

Query: 57  ESGTGKYLPKDGNSRQSDTSTVS-IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
             G    +PK+  +    +     I    +   G+L    R+  I    G+CS +     
Sbjct: 63  --GVCYPVPKNYCTIPPKSCCKEDILLSVRAPVGRLNVADRQYGIGR--GLCSIRPSSSH 118

Query: 116 PKDVLPELLQGWLLSI-DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
            K         +L +I  + +   +I  G+T      + I N  + +PPL EQ  I   +
Sbjct: 119 DKKY-------FLYTILFLEEYFHSISTGSTYEAISTEQIKNTILFLPPLPEQQAIASFL 171

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             E  +ID LI E+ R I LL EK+QA++S+ VTKGLNP+  MKDSGI W+G+V + WE+
Sbjct: 172 DRECGKIDALIAEQERLIALLAEKRQAVISHAVTKGLNPNAPMKDSGIPWIGMVSEEWEI 231

Query: 235 KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-----KPESYETYQIVDPG 289
                +  E+N    + +   ILS+S    +   E  +  L     + +    Y  V PG
Sbjct: 232 VRLGTIFEEVNESGNENLP--ILSVSIHTGVSDEELSDEKLDRKVTRSDDRSKYIAVRPG 289

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGID---STYLAWLMRSYDLCKVF 346
           ++ +    ++  +    + QVM  G+++ AY+  +P  I    + ++  L+R+ +     
Sbjct: 290 DLTYNM--MRAWQGGFGTVQVM--GMVSPAYVVARPKNISRQKTDFIELLLRTPNAISEM 345

Query: 347 --YAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
             Y+ G +  R  L +E+ K++ + +P +KEQ +I N +  +T   D L      +I LL
Sbjct: 346 KRYSRGVTDFRLRLYWEEFKKICIPLPILKEQDEILNFLKEKTGHFDALATTARNAITLL 405

Query: 404 KERRSSFIAAAVTGQIDLRGESQ 426
           KERR++ I+AAVTG+ID+R +S+
Sbjct: 406 KERRAALISAAVTGKIDVRAQSK 428


>gi|229829856|ref|ZP_04455925.1| hypothetical protein GCWU000342_01962 [Shuttleworthia satelles DSM
           14600]
 gi|229791154|gb|EEP27268.1| hypothetical protein GCWU000342_01962 [Shuttleworthia satelles DSM
           14600]
          Length = 407

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/204 (44%), Positives = 127/204 (62%), Gaps = 1/204 (0%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           MKDSGI+W+G VP  W V+  + L T +N KN+ L E N+LSLSYG I +K      GL 
Sbjct: 10  MKDSGIKWIGEVPASWNVRTLYQLATRVNNKNSDLAEQNLLSLSYGKIKRKDINTKDGLL 69

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAW 335
           P S++ Y I++ G+IV R  DLQND  SLR  Q  ERGIITSAY  ++P +  ++ YL +
Sbjct: 70  PASFDGYNIIEAGDIVLRLTDLQNDHTSLRVGQATERGIITSAYTTLQPINPSNARYLYY 129

Query: 336 LMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           L+ ++DL K FY MGSG+RQ L +++VK L  ++P   EQ  I + ++    +ID+++E+
Sbjct: 130 LLHAFDLKKGFYGMGSGVRQGLNYDEVKELRSVLPSQIEQDAIVSYLDDVCQQIDLIIEE 189

Query: 396 IEQSIVLLKERRSSFIAAAVTGQI 419
            + SI   K  R S I    T  I
Sbjct: 190 AKSSIEGYKGWRLSTIKEVTTHGI 213



 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 93/443 (20%), Positives = 160/443 (36%), Gaps = 77/443 (17%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRF-TKLNTGRTSESGKDIIYIGLEDVESGTGKYLP 65
           Y   KDSG++WIG +P  W V  + +  T++N   +  + ++++ +         GK   
Sbjct: 7   YTDMKDSGIKWIGEVPASWNVRTLYQLATRVNNKNSDLAEQNLLSLSY-------GKIKR 59

Query: 66  KDGNSRQ----SDTSTVSIFAKGQILYGKLGPYLRKAII-----------ADFDGICSTQ 110
           KD N++     +     +I   G I+       LR   +           A   GI ++ 
Sbjct: 60  KDINTKDGLLPASFDGYNIIEAGDIV-------LRLTDLQNDHTSLRVGQATERGIITSA 112

Query: 111 FLVLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
           +  LQP +        +LL + D+ +    +  G      ++  +  +   +P   EQ  
Sbjct: 113 YTTLQPINPSNARYLYYLLHAFDLKKGFYGMGSGVRQG-LNYDEVKELRSVLPSQIEQDA 171

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +     +ID +I E    IE  K  + + +  + T G++ DV+M D+ I W   +P
Sbjct: 172 IVSYLDDVCQQIDLIIEEAKSSIEGYKGWRLSTIKEVTTHGISKDVEMVDTEISWAKSIP 231

Query: 230 DHWEVKP--FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
            +W +    +FA               +I     G   +K E                + 
Sbjct: 232 SNWNIGKGHYFASTYSGRAIPGDGTTGSIPVYGSGGSFKKTENP--------------LY 277

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH-GIDSTYLAWLMRSYDLCKVF 346
            GE V                    +G +       +P   +D+ Y A     + L K  
Sbjct: 278 AGEAVL----------------FGRKGTLGKPIYVNRPFWAVDTIYYAVCNEKWMLPKYL 321

Query: 347 YAMGSGLRQSLKFEDVKRLPVLV-----------PPIKEQFDITNVINVETARIDVLVEK 395
           Y M + +     F     LP +V           PPI EQ  I   ++      D  +E 
Sbjct: 322 YYMLT-IFDWESFITHTALPSIVANEVFSSVFICPPISEQLQIIKKLDCVCDNADTAIEA 380

Query: 396 IEQSIVLLKERRSSFIAAAVTGQ 418
            E  I  L+  + S I  AVTG+
Sbjct: 381 TEHLIEELELYKRSLIYEAVTGK 403


>gi|114778243|ref|ZP_01453115.1| HsdS protein [Mariprofundus ferrooxydans PV-1]
 gi|114551490|gb|EAU54045.1| HsdS protein [Mariprofundus ferrooxydans PV-1]
          Length = 462

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 130/444 (29%), Positives = 222/444 (50%), Gaps = 32/444 (7%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES-GKDIIYIGLEDVESGTGK 62
           Y  YP+YKDSGV+W+G IP HW +   K  ++L   +   S  K+  +I +E ++  T  
Sbjct: 5   YPPYPEYKDSGVEWLGEIPAHWVLTRTKYISELTPKKPKISRDKECSFIPMEKLK--TDS 62

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA------DFDGICSTQFLVLQP 116
            +  +  +        + FA   +L  K+ P      IA      +  G  S++  V++ 
Sbjct: 63  IVLDEVRTIDDVYDGYTYFADSDVLMAKVTPCFENKNIAIAQDLVNGVGFGSSEIYVIRA 122

Query: 117 KDVLPELLQGWLLSIDVTQRIE--AICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
              +      + L  D    I   A+     +       + N    +P   EQ+ I   +
Sbjct: 123 NQRVSNRFLFYRLQEDSFMEIAIAAMTGAGGLKRVPSDVLNNYIAAVPQHDEQMEIANFL 182

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             ET +IDTLI ++ + I+LLKEK+QA++S+ VTKGLNPD  M++SGIEW+G VP HWE+
Sbjct: 183 DRETAKIDTLIEKQQQLIKLLKEKRQAVISHAVTKGLNPDAPMRNSGIEWLGEVPAHWEI 242

Query: 235 KPFFALVTELNR------KNTKLIESNILSLSYGNII-QKLETRNMGL--KPESYETYQI 285
                  +   R      K  + ++   + L+  NI  +K++  N+    K    E+ +I
Sbjct: 243 SSLGFECSVKARLGWKGLKAEEYVDEGYIFLATPNIKGEKIDFENVNYITKARYDESPEI 302

Query: 286 -VDPGEIVFRFIDLQNDKRSLRSAQVMER----GIITSAYMAVKPHG-IDSTYLAWLMRS 339
            ++ G+++     +  D  +  +  ++        + S+   ++  G IDS+YL +   S
Sbjct: 303 MLNEGDVL-----VTKDGSTTGTTNIVRELPSPATVNSSIAVLRSVGRIDSSYLYYFFVS 357

Query: 340 YDLCKVFYAMGSGLRQSLKFE-DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
             +  V   +  G+     F+ D+++  VL+PP KEQ +I   I++   + D L+ K E 
Sbjct: 358 TYVQNVIKRIQGGMGVPHLFQADLRKFNVLMPPFKEQKEIAAEIDMRLPKFDDLIAKAEY 417

Query: 399 SIVLLKERRSSFIAAAVTGQIDLR 422
           SI+L+KERR++ I+AAVTG+ID+R
Sbjct: 418 SILLMKERRTALISAAVTGKIDVR 441


>gi|310830282|ref|YP_003965382.1| type I restriction enzyme, S subunit [Ketogulonicigenium vulgare
           Y25]
 gi|308753188|gb|ADO44331.1| type I restriction enzyme, S subunit [Ketogulonicigenium vulgare
           Y25]
          Length = 300

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 105/295 (35%), Positives = 167/295 (56%), Gaps = 14/295 (4%)

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
           R+     GA M  A+W  +G+I +P PPL EQ  I   +  ET RID LI ++ RFIELL
Sbjct: 9   RVNGSTTGAKMPRAEWGFVGSIKVPTPPLEEQTAIAIFLDRETARIDGLIKKKGRFIELL 68

Query: 196 KEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESN 255
           KEK+ AL+++ VTKG++  V MKDSG +W+G +P+HW+  P  AL TE   +  +  +  
Sbjct: 69  KEKRAALITHAVTKGIDAGVPMKDSGQDWLGQIPEHWDTVPPTALFTESKERAHEGDQML 128

Query: 256 ILSLSYGNI----IQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVM 311
             +  YG I     + LE R + +   + +  +  + G+ V   I +++    L  A+ +
Sbjct: 129 SATQKYGVIPLEEFEALEQRQVTMAVTNLDKRKHTEIGDFV---ISMRSMDGGLERARAV 185

Query: 312 ERGIITSAYMAVK--PHGIDSTYLAWLMRSYDLCKVFYAMGSGLR--QSLKFEDVKRLPV 367
             G + S+Y  ++  P  ++  +  +L++S    +      S +R  Q + F   +++ +
Sbjct: 186 --GSVRSSYSVLRCGPE-VEGRFFGYLLKSSLYIQALRLTTSFIRDGQDMNFSHFRKVKL 242

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
              P+ EQ  I + I+ ETARID LV K ++SI LLKE+RS+ I AAVTG+ID+R
Sbjct: 243 PRVPVDEQIRIADHIDRETARIDGLVAKTDRSIELLKEKRSTLITAAVTGKIDVR 297


>gi|120553353|ref|YP_957704.1| restriction modification system DNA specificity subunit
           [Marinobacter aquaeolei VT8]
 gi|120323202|gb|ABM17517.1| restriction modification system DNA specificity domain
           [Marinobacter aquaeolei VT8]
          Length = 439

 Score =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 131/437 (29%), Positives = 202/437 (46%), Gaps = 48/437 (10%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           YP+YK SGVQW+G +P +WK+  +K   ++  G+  +S           VES      P 
Sbjct: 6   YPEYKGSGVQWLGEVPSNWKIGRLKHLLRIRGGQDYKS-----------VESYVPTDFPV 54

Query: 67  DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
            G+  Q   +T  ++    +L G+ G   +   +        T F      +VLP     
Sbjct: 55  IGSGGQFTYATDYLYDGESVLLGRKGTIDKPLYVKGKFWTVDTMFYT----EVLPGTNGR 110

Query: 127 WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
           +   +  T   +       +       + N  +P+PP  EQ  I   +  ET +ID LI 
Sbjct: 111 YAYYLATTIPFDLYSTNTALPSMSQFDLANHGLPLPPKCEQTQIARFLDHETAKIDALIR 170

Query: 187 ERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF--FALV--- 241
           E+ R IELL+EK+QA++S+ VTKGL+PDV MKDSG+EW+G VP HW V     FA V   
Sbjct: 171 EQERLIELLQEKRQAVISHAVTKGLDPDVPMKDSGVEWLGEVPAHWIVARIKNFARVESG 230

Query: 242 -TELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
            T   +K    ++ +I  +S  +  Q        LK   Y    I D    V       +
Sbjct: 231 HTPDKKKEEYWVDCDIPWVSLNDSKQ--------LKKADY----IADTSTKVNDLGIANS 278

Query: 301 DKRSLRSAQVM--ERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK-----VFYAMGSGL 353
             R L +A V+      I  + +  KP  +    +AWL     L       +FYAM S  
Sbjct: 279 SARLLPAAAVVFTRDASIGLSAITTKPMAVSQHLIAWLCAGEKLVPEYLLLIFYAMESEF 338

Query: 354 R--------QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
                    +++  +DV+ L    PP++EQ  +      +   +   ++  E++I+LLKE
Sbjct: 339 ERYTFGATIKTIGMDDVRSLTAAFPPMEEQKQLVTWAFRKKETLQAGLDAAEKTILLLKE 398

Query: 406 RRSSFIAAAVTGQIDLR 422
           RRS+ I++AVTG+ID+R
Sbjct: 399 RRSALISSAVTGKIDVR 415


>gi|16124874|ref|NP_419438.1| type I restriction-modification system, S subunit [Caulobacter
           crescentus CB15]
 gi|221233594|ref|YP_002516030.1| type I restriction-modification system specificity subunit
           [Caulobacter crescentus NA1000]
 gi|13421830|gb|AAK22606.1| type I restriction-modification system, S subunit [Caulobacter
           crescentus CB15]
 gi|220962766|gb|ACL94122.1| type I restriction-modification system specificity subunit
           [Caulobacter crescentus NA1000]
          Length = 450

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 136/469 (28%), Positives = 210/469 (44%), Gaps = 78/469 (16%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE--------------SGKDII 49
           + AY  YK+SGV+W+G +P HW   P+K    + +G T                S KD+ 
Sbjct: 3   FPAYESYKESGVEWLGRVPSHWNFRPLKHLVIMRSGGTPSKEREDYWGGEIPWASAKDLK 62

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKA----IIADFDG 105
              L D +         +G ++    + V +  +G +L  +  P  R +    I  D  G
Sbjct: 63  VDTLTDTQDHLTAEALDEGAAQLLPANAVVVLVRGMML-ARTFPVCRLSRPMTINQDLKG 121

Query: 106 ICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHAD----WKGIGNIPMPI 161
           + +        + V P  L  W L       +E +C      H            + +P 
Sbjct: 122 LIAN-------RGVDPNYL-AWSLR---ASEVETLCRLDEAGHGTKALRMDAWSTMELPA 170

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           P LAEQ  I   +  ET +ID L+  + R I LLKEK+QA++S+ VTKGL+P  +MKDSG
Sbjct: 171 PSLAEQQAIAAFLDRETAKIDALVEAQERLIALLKEKRQAVISHAVTKGLDPSAQMKDSG 230

Query: 222 IEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE 281
           +EW+G +P HWEV P             K +  +I +  +G+ + K    + G +   Y 
Sbjct: 231 VEWLGQMPAHWEVVP------------AKNLADSIKAGPFGSALTKDMYSSAGYR--VYG 276

Query: 282 TYQIVDPGEIVFRFID--LQNDKRSLRS-----------------------AQVMERGII 316
             Q++ PG+  FR  D  + +D+ +  S                        Q  E GII
Sbjct: 277 QEQVI-PGD--FRIGDYYVTSDRYNELSQYRVEVGDLLVSCVGTFGKIAIFPQGAEPGII 333

Query: 317 TSAYMAVKPHG-IDSTYLAWLMRSYDLCKVF-YAMGSGLRQSLKFEDVKRLPVLVPPIKE 374
               +  +P+  +D TYL  L+RS    + F Y    G    +    +  + V VPP++E
Sbjct: 334 NPRLIRFRPNNQVDPTYLCVLLRSAVSFEQFSYLSRGGTMDVINIGILGEIVVPVPPMQE 393

Query: 375 QFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           Q  I   +     + D L    E +I LL+ERR++ I+AAVTG+ID+RG
Sbjct: 394 QISIAGYLAEVQEQFDSLSAASEAAITLLQERRAALISAAVTGKIDVRG 442


>gi|298674425|ref|YP_003726175.1| restriction modification system DNA specificity domain-containing
           protein [Methanohalobium evestigatum Z-7303]
 gi|298287413|gb|ADI73379.1| restriction modification system DNA specificity domain protein
           [Methanohalobium evestigatum Z-7303]
          Length = 461

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 144/456 (31%), Positives = 238/456 (52%), Gaps = 46/456 (10%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTS---ESGK-DIIYIGLEDVES 58
           +K YP+YKDSG++W+G IP+HW V  ++R  K L  G T+   +SG  +     +E + +
Sbjct: 18  FKPYPEYKDSGIEWLGEIPEHWDVKQLRRVIKSLKNGTTAPQLDSGTTNYPVTRIETISN 77

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGP--YLRK-AIIADFDGICS-TQFLVL 114
           G   Y    G  +++D     I  K  IL   +    Y+   AI  D + +      L L
Sbjct: 78  GYINY-NNVGYLKENDVDKRYILNKDDILISHINSLEYIGNCAIYKDNETLVHGMNLLRL 136

Query: 115 QPKD-VLPELLQGWLLSIDV--TQRIEA--ICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
            P D ++P+ L  +L S +   + RI A      A++S    K +     P     EQ  
Sbjct: 137 IPDDNIIPDFLIYYLKSKNFKYSARIHAKPAINQASVSSTVLKSL-KFSYP-SNFNEQKS 194

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  ET +ID LI ++ R +ELL+EK+ AL+++ V KGL+PDV+MKDSGIEW+G +P
Sbjct: 195 IANFLDKETHKIDKLIEKKQRLVELLEEKRSALINHTVAKGLDPDVEMKDSGIEWLGEIP 254

Query: 230 DHWEVKPFFAL----VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQI 285
           +HW+V     L    VT+   ++   +++ I  LS  +I      +N  LK   +E  + 
Sbjct: 255 EHWDVVKLKYLLRSKVTDGPHESPAFVDNGIPFLSADSI------QNGKLK---FENCRY 305

Query: 286 VDPGEIVFRFI-DLQNDKRSL---RSAQVMERGIIT--------SAYMAVKP--HGIDST 331
           V P E   R+I   + +K  L   ++A V +  ++         S    +KP    ++S 
Sbjct: 306 V-PYEDHIRYIRKCKPEKYDLLLGKAASVGKVALVDVDFEFSIWSPLALIKPDTRELNSK 364

Query: 332 YLAWLMRSYDLCKVFYAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
            L +++RS  + K    +  +  + +L  ++++ L +++P + EQ  I + ++  T++ID
Sbjct: 365 LLYYVLRSRYVQKQIDMLNHTNTQDNLGMKEIENLKIILPSVSEQKQIADYLDQRTSKID 424

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
            L+ KI   I  LKE R++ I+AAVTG+ID+RGE Q
Sbjct: 425 ELINKINHQIEYLKEYRTALISAAVTGKIDVRGEEQ 460



 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 111/249 (44%), Gaps = 37/249 (14%)

Query: 194 LLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT---------EL 244
           +++E++Q    +  T G  P  + KDSGIEW+G +P+HW+VK    ++          +L
Sbjct: 4   VVQEQRQ---KFFDTSGFKPYPEYKDSGIEWLGEIPEHWDVKQLRRVIKSLKNGTTAPQL 60

Query: 245 NRKNTKLIESNILSLSYGNIIQKLETRNMG-LKPESYETYQIVDPGEIVFRFID------ 297
           +   T    + I ++S G I       N+G LK    +   I++  +I+   I+      
Sbjct: 61  DSGTTNYPVTRIETISNGYI----NYNNVGYLKENDVDKRYILNKDDILISHINSLEYIG 116

Query: 298 ---LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRS--YDLCKVFYAMGSG 352
              +  D  +L     + R         +    I   +L + ++S  +      +A  + 
Sbjct: 117 NCAIYKDNETLVHGMNLLR--------LIPDDNIIPDFLIYYLKSKNFKYSARIHAKPAI 168

Query: 353 LRQSLKFEDVKRLPVLVPP-IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
            + S+    +K L    P    EQ  I N ++ ET +ID L+EK ++ + LL+E+RS+ I
Sbjct: 169 NQASVSSTVLKSLKFSYPSNFNEQKSIANFLDKETHKIDKLIEKKQRLVELLEEKRSALI 228

Query: 412 AAAVTGQID 420
              V   +D
Sbjct: 229 NHTVAKGLD 237


>gi|149175698|ref|ZP_01854317.1| type I restriction-modification system, S subunit [Planctomyces
           maris DSM 8797]
 gi|148845417|gb|EDL59761.1| type I restriction-modification system, S subunit [Planctomyces
           maris DSM 8797]
          Length = 450

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 130/448 (29%), Positives = 220/448 (49%), Gaps = 37/448 (8%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD-------IIYIGLEDV 56
           +  Y +YK+SG++W+G +P+HW V  +     +     +ESG D        I+ G+ D 
Sbjct: 3   FPKYAEYKESGIEWLGKVPEHWDVFRMG----ILFAEVAESGNDDLPVLQVSIHHGVSDR 58

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
           E    +   K   +R  D S         ++Y  +  +         +G+ S  ++V +P
Sbjct: 59  ELSESESDRK--ITRIDDKSKYKRVVPNDLVYNMMRAWQGGFGTVKVEGMVSPAYVVARP 116

Query: 117 K-DVLPELLQGWLLSIDVTQRIEAICEGATMSHAD--WKGIGNIPMPIPPLAEQVLIREK 173
           K D   + ++    +    +++     G T       W    N+ + +P  +EQ  I + 
Sbjct: 117 KIDFQTQFIEHLFRTPQAIEQMRRYSHGVTDFRLRLYWDKFKNVRVALPDKSEQQEICDY 176

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           I  ET +ID L+ E+ R IELLKEK+QA++S+ VTKGLNP+  MKDSGIEW+G VP+HWE
Sbjct: 177 IDVETSKIDALVAEQRRLIELLKEKRQAVISHAVTKGLNPNAPMKDSGIEWLGDVPEHWE 236

Query: 234 VKPF--FALVTELNR-----KNTKLIESNILSLSYGNII-QKLETRNMGLKPESYETYQI 285
           V     +A   + +R         L    IL LS  NI+  KL+ +    K  S+E +  
Sbjct: 237 VCSLRRYAFFVDGDRGSEYPNENDLTSDGILFLSSKNIVGGKLDLKES--KFISHEKFDA 294

Query: 286 VDPGEIVFRFIDLQNDKRSLR---------SAQVMERGIITSAYMAVKP-HGIDSTYLAW 335
           ++ G+     + ++    + R          A   E   I +  M ++  + +   YL+ 
Sbjct: 295 LNRGKAQDGDLIVKVRGSTGRIGEMALFDVGAYSFETAFINAQMMIIRTGNKLTPKYLSK 354

Query: 336 LMRS-YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           + +S Y + ++        +Q L  +    L V +PP+ EQ +I + I+++    D L  
Sbjct: 355 VSQSIYWMEQLSVGAYGTAQQQLSNKVFSDLFVTMPPVTEQAEIADFIDLKVGEFDSLET 414

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           + EQ+I LL+ERR++ I+AAVTG+I++R
Sbjct: 415 EAEQAIELLQERRTALISAAVTGKINVR 442


>gi|294789183|ref|ZP_06754422.1| restriction modification system DNA specificity domain protein
           [Simonsiella muelleri ATCC 29453]
 gi|294482924|gb|EFG30612.1| restriction modification system DNA specificity domain protein
           [Simonsiella muelleri ATCC 29453]
          Length = 436

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 124/439 (28%), Positives = 210/439 (47%), Gaps = 27/439 (6%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNT---GRTSESGKDIIYIGLEDVESGTGKY 63
           Y +YKDSG+ W+G +P+HW +  +K     N    G  +++  +I+Y+ +  V    G  
Sbjct: 4   YEKYKDSGIAWLGEVPEHWSICRLKDEVTFNDEVLGDKTDTDYEILYVDISSVSLIEGII 63

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII----ADFDGICSTQFLVLQPK-D 118
             +      S +    I   G ++   +  YL KAI     A+ + I ST F VL+PK +
Sbjct: 64  QKELMTFENSPSRARRIVKNGDVIVSTVRTYL-KAITQIQDAEDNLIVSTGFAVLRPKEN 122

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           + P  L  W+ S ++   I +   G +    +   +  +P+   PL EQ  I   +  + 
Sbjct: 123 LFPRFLGYWVQSENMIGAIVSNSVGVSYPAINATDLVRLPIVKLPLKEQTAIAHYLDTKL 182

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF- 237
             ID LI ++   +E L E++ A++++ VTKGLNP   MK+SG+EW+G VP HW+V PF 
Sbjct: 183 GEIDALIDKQQTLLEKLAERRTAVITHAVTKGLNPAAPMKNSGVEWLGDVPAHWDVSPFK 242

Query: 238 --FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
                + +   K  +   S +  ++  NI   +    +  +    + Y+     E++ R 
Sbjct: 243 LVMNSIIDYRGKTPEKTNSGVFLITARNIKNGIIDYTLSQEFIDEDNYE-----EVMRRG 297

Query: 296 ID-----LQNDKRSLRSAQVMERGIITSAYMAVKPHG----IDSTYLAWLMRSYDLCKVF 346
           +      L   +  L     ++R  +  A   +K  G    +D+ +L + + S       
Sbjct: 298 LPKLGQVLMTTEAPLGEVAQIDRTDVALAQRVLKFDGKKDKLDNRFLKYFILSKAFQASL 357

Query: 347 YAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
           Y   +G     +K E +  L  L+PP+ EQ  I N ++ ETA+ID L E + Q+I  LKE
Sbjct: 358 YKFATGSTALGIKSERLSYLKSLLPPVTEQTAIANYLDQETAKIDRLCETVNQTIGRLKE 417

Query: 406 RRSSFIAAAVTGQIDLRGE 424
            R++ I  AVTG+I +  E
Sbjct: 418 YRTALITQAVTGKIKVTDE 436



 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 105/217 (48%), Gaps = 16/217 (7%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT-------ELNRKNTKLIESNILSLSY-G 262
           +N   K KDSGI W+G VP+HW +      VT       +    + +++  +I S+S   
Sbjct: 1   MNRYEKYKDSGIAWLGEVPEHWSICRLKDEVTFNDEVLGDKTDTDYEILYVDISSVSLIE 60

Query: 263 NIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA 322
            IIQK     M  +       +IV  G+++   +  +   +++   Q  E  +I S   A
Sbjct: 61  GIIQK---ELMTFENSPSRARRIVKNGDVIVSTV--RTYLKAITQIQDAEDNLIVSTGFA 115

Query: 323 V-KP-HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDIT 379
           V +P   +   +L + ++S ++     +   G+   ++   D+ RLP++  P+KEQ  I 
Sbjct: 116 VLRPKENLFPRFLGYWVQSENMIGAIVSNSVGVSYPAINATDLVRLPIVKLPLKEQTAIA 175

Query: 380 NVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           + ++ +   ID L++K +  +  L ERR++ I  AVT
Sbjct: 176 HYLDTKLGEIDALIDKQQTLLEKLAERRTAVITHAVT 212


>gi|257061739|ref|YP_003139627.1| restriction modification system DNA specificity domain protein
           [Cyanothece sp. PCC 8802]
 gi|256591905|gb|ACV02792.1| restriction modification system DNA specificity domain protein
           [Cyanothece sp. PCC 8802]
          Length = 456

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 136/454 (29%), Positives = 223/454 (49%), Gaps = 44/454 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTSESGKDIIYI-------G 52
           +K +K YP YK SGV W+G IP  W+V  ++  +K +  G    +    IY        G
Sbjct: 6   LKQWKLYPNYKPSGVDWLGDIPDSWEVKRLRYLSKKITAGPFGSNLTKNIYTSTGYKIYG 65

Query: 53  LEDVESGTGK----YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF--DGI 106
            E V +        Y+ K+   + S     S    G IL   +G + + A++      GI
Sbjct: 66  QEQVIASDFSIGDYYISKEKYDQMSQYKINS----GDILISCVGTFGKVAVVPKNIEQGI 121

Query: 107 CSTQFLVLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
            + + + L P  + +    L+  L S+   +++E +  G TM   +   + +I +PIPPL
Sbjct: 122 INPRLIKLIPITEYINSVYLEKLLKSVVAFEQMEKLSRGGTMGVINIGLLSDILLPIPPL 181

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
            EQ  I + +  ET +ID LIT + R IELLKEK+ AL+S+ VTKGLNPDV MKDSG+EW
Sbjct: 182 PEQEKIAQFLDKETAKIDKLITLKERLIELLKEKRTALISHAVTKGLNPDVPMKDSGVEW 241

Query: 225 VGLVPDHWEVKPFFALVTELN-----RKNTKLIESNILSLSYGNIIQ-KLETRNM-GLKP 277
           +G +P+HWEVK    +V  +            +ES I  L   NI   K++  N+  +  
Sbjct: 242 LGFIPEHWEVKRLKYIVPNITVGIVVTPAKYYVESGIPCLRSVNISSGKIDNSNLVFISS 301

Query: 278 ESYETYQ--IVDPGEIVFRFIDLQNDKR----SLRSAQVMERGIITSA---YMAVKPHGI 328
           +S E +Q   +  G++V     +         +   A  ++  II ++         + +
Sbjct: 302 QSNELHQKSKIYKGDLVLVRTGVTGTAAIVTDNFDGANCVDLLIIRNSRLILTLYLYYYL 361

Query: 329 DSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
           +S+  ++ + +Y +          ++       +  L +  PP +EQ  I   ++ +T +
Sbjct: 362 NSSTTSYQVNNYSV--------GAIQAHYNTSTLSELIITFPPPQEQQKIAEYLDRKTEQ 413

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           ID ++ K  +SI  LKE R+  I+AAVTG+ID+R
Sbjct: 414 IDQIINKTRESIEYLKEYRTVLISAAVTGKIDVR 447


>gi|209523387|ref|ZP_03271942.1| restriction modification system DNA specificity domain [Arthrospira
           maxima CS-328]
 gi|209496129|gb|EDZ96429.1| restriction modification system DNA specificity domain [Arthrospira
           maxima CS-328]
          Length = 415

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 99/300 (33%), Positives = 171/300 (57%), Gaps = 11/300 (3%)

Query: 127 WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
           WL S  + + +E    G+TM H  W   GN P+ +PP+ EQ  I   +  ET +ID LI 
Sbjct: 121 WLASWFI-KELEHKAHGSTMQHLTWNAFGNFPVLLPPMPEQKAIAHYLDKETAKIDQLIE 179

Query: 187 ERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNR 246
            + R +ELL EK++AL+++ VT+GLNPDV M+DSG+EW+G +P HW+V+    L  E++ 
Sbjct: 180 AKKRLLELLDEKRRALITHAVTRGLNPDVPMRDSGVEWIGEIPKHWKVEFAKWLFKEIDD 239

Query: 247 KNTKLIESNILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPGEIVFRFIDLQNDKRSL 305
           ++T   E  +L++S+   I     +++ + K ES E Y++   G+++   +        +
Sbjct: 240 RSTTGQEE-LLTVSHITGITPRSEKDVNMFKAESMEGYKVCQSGDLIINTLWAWMGAMGV 298

Query: 306 RSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCK--VFYAMGSGL-RQSLKFED 361
                 + GI++ +Y   +P G     YL +L+R     +  + Y+ G  + R  L  E+
Sbjct: 299 S----FQPGIVSPSYHVYRPQGEYHPVYLDYLVRIPIFAEEAIRYSKGVWISRLRLYPEE 354

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
             ++ + VPP++EQ+ I   +  +T ++D L    ++++ LL+ERR+S I AAVTGQ+ +
Sbjct: 355 FFQILLPVPPLEEQYKIGKYLMEKTKKLDNLSIATKKTMDLLQERRTSLITAAVTGQLKI 414



 Score = 61.2 bits (147), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 101/206 (49%), Gaps = 9/206 (4%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           +DSGV+WIG IPKHWKV   K   K    R++   ++++ +      +G      KD N 
Sbjct: 211 RDSGVEWIGEIPKHWKVEFAKWLFKEIDDRSTTGQEELLTVSH---ITGITPRSEKDVNM 267

Query: 71  RQSDT-STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLL 129
            ++++     +   G ++   L  ++    ++   GI S  + V +P+     +   +L+
Sbjct: 268 FKAESMEGYKVCQSGDLIINTLWAWMGAMGVSFQPGIVSPSYHVYRPQGEYHPVYLDYLV 327

Query: 130 SIDVTQRIEAI--CEGATMSHADW--KGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
            I +    EAI   +G  +S      +    I +P+PPL EQ  I + ++ +T ++D L 
Sbjct: 328 RIPIFAE-EAIRYSKGVWISRLRLYPEEFFQILLPVPPLEEQYKIGKYLMEKTKKLDNLS 386

Query: 186 TERIRFIELLKEKKQALVSYIVTKGL 211
               + ++LL+E++ +L++  VT  L
Sbjct: 387 IATKKTMDLLQERRTSLITAAVTGQL 412


>gi|144900420|emb|CAM77284.1| type I restriction-modification system, S subunit [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 431

 Score =  160 bits (406), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 134/446 (30%), Positives = 205/446 (45%), Gaps = 50/446 (11%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTG------RTSESGKDIIYIGLEDV 56
           +  Y  YKDSGV+W+G +P HW V P+KR    L +G        S+ G   I IG    
Sbjct: 3   FPQYADYKDSGVEWLGEVPGHWDVFPLKRDLAFLTSGSRGWAEHYSDDGALFIRIG---- 58

Query: 57  ESGTGKYLPKDG-NSRQSDTSTVSI----------FAKGQILYGKLGPYLRKAIIA--DF 103
                  L +DG +   SD   V +             G +L+  +  YL    +A  + 
Sbjct: 59  ------NLTRDGIHLDLSDIQRVEVPDGAEGERTRVVGGDVLF-SITAYLGSVAVAPEEL 111

Query: 104 DGICSTQFLVL---QPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
           +    +Q + L     +  +P  +    LS      +     G T        + N+ M 
Sbjct: 112 EVAYVSQHVALARLHQRRFIPAWVGYVTLSNIGETYLGTQGYGGTKVQLSLDDVANLIMT 171

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
            PPL EQ  I   +  +T +ID L+ E+ R + LL EK+QA++S+ VTKGLNP   MKDS
Sbjct: 172 APPLPEQSAIAAFLDRQTGKIDALVAEQERLLTLLAEKRQAVISHAVTKGLNPAAPMKDS 231

Query: 221 GIEWVGLVPDHWEVKP--FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPE 278
           GIEW+G VP+HW+V P  +F      +  +   +E+         +I           P 
Sbjct: 232 GIEWLGEVPEHWKVIPLRWFCTCKSGDSISADGVEAECDEDRTAPVIGGNGVMGYTYAP- 290

Query: 279 SYETYQIVDPGEIVFRFIDLQNDKRSLR-SAQVMERGIITSAYMAVKPHGIDSTYLAWLM 337
                 I  P  ++ R   L  +  S++  A V +  +I      V     +  YL+ L+
Sbjct: 291 -----NITHPVLVIGRVGALCGNVHSIKLPAWVTDNALILDIAEGV----FNQEYLSHLL 341

Query: 338 RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           RS +L ++       L    +  D +R+P  + P+ EQ  I   +N +TA+ID L  +  
Sbjct: 342 RSRNLNEIASKTAQPLITGSQVRD-QRIP--LAPMDEQSAIVEFLNEQTAKIDTLTAEAL 398

Query: 398 QSIVLLKERRSSFIAAAVTGQIDLRG 423
           ++I LLKE RS+ I+AAVTG+ID+RG
Sbjct: 399 RAIALLKEHRSALISAAVTGKIDVRG 424


>gi|300724721|ref|YP_003714046.1| type I restriction-modification [Xenorhabdus nematophila ATCC
           19061]
 gi|297631263|emb|CBJ91958.1| Type I restriction-modification [Xenorhabdus nematophila ATCC
           19061]
          Length = 429

 Score =  159 bits (403), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 133/436 (30%), Positives = 214/436 (49%), Gaps = 48/436 (11%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M  Y+AYP+YKDSGV+W+G IPKHW V  +K    +  G+  +            V+S  
Sbjct: 1   MGKYRAYPEYKDSGVEWLGKIPKHWNVCRLKHLIIIRNGQDYKM-----------VQSDA 49

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           G   P  G+  Q   ST  ++ K  +L G+ G   +   + +      T +      DV 
Sbjct: 50  G--YPVIGSGGQFAFSTQYMYDKPSVLLGRKGTIDKPLYVNEPFWTVDTMYYTEMRDDVD 107

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP-PLAEQVLIREKIIAETV 179
            +    +L  + VT + +       +     + +GN    +   + E++LI   +  ET 
Sbjct: 108 AK----YLYYLAVTIQFDRYSTSTALPSMTQENLGNYFFAVSNEITERLLISTFLDHETA 163

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV---KP 236
           +ID LI ++ + I+LLKEK+QA++S+ VTKGLN DV MKDSG+EW+G +P  W++   K 
Sbjct: 164 KIDILIEKQQQLIKLLKEKRQAVISHAVTKGLNLDVPMKDSGVEWLGYIPSEWDIVRLKY 223

Query: 237 FFALVTELNRKNT-KLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
             AL  +   ++T K +    +S   G  I    T+N    PE          G+++F  
Sbjct: 224 IVALTGDKAPQSTEKYVGMENISSKSGKYIM---TKNA--LPEGVS--NSFKKGDVLFGK 276

Query: 296 IDLQNDKRSLRSAQVME-RGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVF------YA 348
           +     +  L  + + E  GI +S ++ +    +   +L + M    L   F        
Sbjct: 277 L-----RPYLAKSWLAEFSGICSSEFLVLHSLKVHPKFLNYYM----LTDAFIDQVNSST 327

Query: 349 MGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
            GS + R S  F  +  LPV +   K    I N +  +T++ID+L+EK ++ I LL+ERR
Sbjct: 328 YGSKMPRASWDF--IGLLPVPITTYKSTEKIANFLGQKTSKIDMLLEKQQKVIKLLQERR 385

Query: 408 SSFIAAAVTGQIDLRG 423
           +S I+AAVTG+ID+R 
Sbjct: 386 TSLISAAVTGKIDIRN 401


>gi|218248669|ref|YP_002374040.1| restriction modification system DNA specificity domain-containing
           protein [Cyanothece sp. PCC 8801]
 gi|218169147|gb|ACK67884.1| restriction modification system DNA specificity domain protein
           [Cyanothece sp. PCC 8801]
          Length = 453

 Score =  159 bits (403), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 135/450 (30%), Positives = 219/450 (48%), Gaps = 39/450 (8%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRF-TKLNTGRTSESGKDI------IYIGL 53
           +K +K YP YK SGV ++G IP  W+V  +K   +K+ +G+T + G +I      I++  
Sbjct: 6   LKQWKPYPHYKPSGVDFLGDIPDGWEVKRLKWIVSKIGSGKTPKGGAEIYSDSGIIFLRS 65

Query: 54  EDVESGTGK-----YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII--ADFDGI 106
           +++     +     Y+ KD +   S +    +     IL    G  L + +I   DF   
Sbjct: 66  QNIHFDGLRLDDVVYINKDIDKAMSSSRVKPL----DILLNITGASLGRCMIIPKDFPSS 121

Query: 107 CSTQFL-VLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
              Q + +L+P    + P  L   + S  +  +I +   G +     +   GN+    P 
Sbjct: 122 NVNQHVCILRPIVTRINPYFLNRVMSSNAIQNQIFSSEVGVSREGLTFAQAGNLISVFPS 181

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
           L EQ  I + +  ET +ID LIT + R IELLKEK+ AL+S+ VTKGLNPDV MKDSG+E
Sbjct: 182 LPEQEKIAQFLDEETAKIDKLITHKQRLIELLKEKRTALISHAVTKGLNPDVPMKDSGVE 241

Query: 224 WVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI----IQKLETRNMGLKPES 279
           W+G +P+HWEVK    L       + + I+  I     G      I  +   N  L    
Sbjct: 242 WLGFIPEHWEVKKIKRLSLVKRGASPRPIDDPIYFDDNGEYVWVRISDVTASNKYLLEAE 301

Query: 280 YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI-------DSTY 332
            +  +I        + + LQ ++  L     + + IIT     +    +       +  Y
Sbjct: 302 QKLSEIGK-----RKSVPLQPNELFLSICASVGKPIITKIKCCIHDGFVYFPELKENREY 356

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           L ++    +L K    MG+ L  +L  E +  + + +PP+ EQ  I   ++ +T +ID +
Sbjct: 357 LYYIFLGGELYKGLGKMGTQL--NLNTEIIGDVKLPIPPVSEQQKIAEYLDEKTEQIDPI 414

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           ++K  +SI  LKE R++ I+AAVTG+ID+R
Sbjct: 415 IKKTRESIEYLKEYRTALISAAVTGKIDVR 444


>gi|283787023|ref|YP_003366888.1| Type I restriction-modification system, specificity (S) subunit
           [Citrobacter rodentium ICC168]
 gi|282950477|emb|CBG90140.1| putative Type I restriction-modification system, specificity (S)
           subunit [Citrobacter rodentium ICC168]
          Length = 446

 Score =  159 bits (402), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 137/460 (29%), Positives = 216/460 (46%), Gaps = 70/460 (15%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES------GKDIIYIGLE 54
           M  YKAYP+YKDSGV+W+G IP HWK++  K       G+   +         + Y+ +E
Sbjct: 1   MAKYKAYPEYKDSGVEWLGEIPIHWKMLRHKYVAFFTKGKNPTNLLEQPLKNTLPYLSME 60

Query: 55  DVESGT-GKYLPKDGNSRQS-DTSTVSIF---AKGQILYGKLGPYLRKAIIADFDGICST 109
            + + T  KY     + R + +   + I+     G+ L GK G        A       +
Sbjct: 61  CLRNNTTDKYALISNDVRVALEGQPLVIWDGSNAGEFLKGKSGILSSTMAAATLIYPLHS 120

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
           Q+               W L I +   +     G  + H +   + +I   IP + EQ  
Sbjct: 121 QYY--------------WYLCISIEPEMRKNAVGMGIPHVNGDELRSISFGIPSIYEQKQ 166

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           + + +  ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPDV MKDSG+EW+G VP
Sbjct: 167 VADFLDHETAKIDNLIEKQQQLIELLKEKRQAVISHAVTKGLNPDVPMKDSGVEWLGDVP 226

Query: 230 DHWEV---KPFFALVTELNRKNTK---LIESNILSLSYGNIIQKLETRNMGLKPESYETY 283
           +HW V   K +  + +      TK    I  NI  +S  +  Q    + +    +++  Y
Sbjct: 227 EHWRVSRIKNYAKIESGHTPSRTKPEYWISCNIPWVSLNDSKQ---LKEIDYIEDTF--Y 281

Query: 284 QIVDPGEIVFRFIDLQNDKRSLRSAQ--VMER------GIITSAYMAVKPHGIDSTYLAW 335
           +I + G        + N    L  A+  V  R        IT+  MAV  H I     AW
Sbjct: 282 KISELG--------MANSSAHLLPARAVVFTRDASIGLSAITTKSMAVSQHLI-----AW 328

Query: 336 LMRSY-----DLCKVFYAMGSGLR--------QSLKFEDVKRLPVLVPPIKEQFDITNVI 382
           +          L  VFYAM             +++  ++V+ L    PP++EQ ++ +  
Sbjct: 329 ICDEKFIIPEFLLLVFYAMEKEFERYTFGATIKTIGMDNVRGLKSTFPPVEEQRNLIDWA 388

Query: 383 NVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
             +  +I   + K+E  + LL+ERR++ I+AAVTG+ID+R
Sbjct: 389 FSKIEKIKSSINKVEDMLSLLQERRTALISAAVTGKIDVR 428


>gi|86152085|ref|ZP_01070297.1| putative type I restriction enzyme specificity protein
           [Campylobacter jejuni subsp. jejuni 260.94]
 gi|85840870|gb|EAQ58120.1| putative type I restriction enzyme specificity protein
           [Campylobacter jejuni subsp. jejuni 260.94]
          Length = 433

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 132/444 (29%), Positives = 206/444 (46%), Gaps = 44/444 (9%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK-----DIIYIGLEDVESGTGKY 63
            +K+SG++W+G IP+HW+VV I +      G   E+       +I  I + D++     Y
Sbjct: 3   NFKESGIEWLGEIPEHWEVVKINKIVTFVNGYAFENFDFNPIFEIPVIRIGDMQKEKILY 62

Query: 64  LPKDGNSRQSDTSTVSIF--AKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
              D   +  +   +  F  +   IL    G    K    D D        V   +  L 
Sbjct: 63  ---DNCLKTKEKEKLKQFLISNNDILIALSGATTGKIAFCDTDNKAYINQRVAIVRSKL- 118

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           +L++ + L+   +  IE  C G+   +   K IG   +P+PPL EQ  I   +  +  +I
Sbjct: 119 KLVKYYFLTRGFSLLIELACNGSAQPNISTKEIGEFKIPLPPLKEQEQIANFLDEKCEQI 178

Query: 182 DTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF---F 238
              I ++ + I LLKE+KQA ++  +TKGL+ ++  KDSGIEW+G +P HWEVK F   F
Sbjct: 179 ANFIEKKEKLISLLKEQKQAFINETITKGLDKNINFKDSGIEWLGEIPQHWEVKKFKMLF 238

Query: 239 ALVTELNRKNTKLIESNILSLSYGNIIQKLETR---NMGLKPESYETYQIVDPGEIV--- 292
            L   LN      +   I  +SYG I  K   R    +   P   +TY    P  ++   
Sbjct: 239 TLGNGLNITKADFVSYGIPCVSYGEIHSKYPCRLNTTIHTLPFVSKTYLADKPQSLLQKG 298

Query: 293 -FRFIDLQND-KRSLRSAQVMERGIITSAYMAV--KPHG-IDSTYLAWLMRSY------- 340
            F F D   D + S     +     I + Y  +  K  G I+S Y ++L  S        
Sbjct: 299 DFVFADTSEDIEGSGNFTSIQSDTPIFAGYHTIILKYKGKINSLYFSFLFDSIFTRNQIR 358

Query: 341 -DLC--KVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            ++C  KVF    S L         K +  L+PP+KEQ  I N ++ +  +ID+L+EK +
Sbjct: 359 KEVCGVKVFSITKSIL---------KEVQCLIPPLKEQEQIANFLDEKCEKIDLLIEKTK 409

Query: 398 QSIVLLKERRSSFIAAAVTGQIDL 421
           + I L+KE +++ I  AV G+I L
Sbjct: 410 KQIKLIKEYKTTLINQAVCGRISL 433


>gi|251791801|ref|YP_003006522.1| restriction modification system DNA specificity domain-containing
           protein [Dickeya zeae Ech1591]
 gi|247540422|gb|ACT09043.1| restriction modification system DNA specificity domain protein
           [Dickeya zeae Ech1591]
          Length = 462

 Score =  158 bits (400), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 137/475 (28%), Positives = 216/475 (45%), Gaps = 70/475 (14%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD-------IIYIGL 53
           M   + Y +YK+S V+W+G +P HW  V +K  ++  +G T +   D       I ++  
Sbjct: 1   MMKQQTYSEYKESDVKWLGQVPVHWNAVSLKWISQRYSGGTPDKSNDAYWENGDIPWLNS 60

Query: 54  EDVESG----TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFD--GIC 107
             V  G       Y+ ++G +    +S+     K  ++    G    K ++A       C
Sbjct: 61  GSVNDGYITEPSTYITREGFA----SSSAKWVPKNALVMALAGQGKTKGMVAQLGIRATC 116

Query: 108 STQFLVLQPKDVL-PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
           +     + PK+   P  L  WL+S    Q I  +  G      +   +G+IP P+ P  E
Sbjct: 117 NQSMAAIIPKEKFTPRFLYWWLVS--NYQNIRNMAGGEQRDGLNLDMLGSIPCPLLPRPE 174

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTK----------GLNPDVK 216
           Q  I + +  ET RID+L+ ++ + I LLKEK+ AL+S+IVT+          GL P  +
Sbjct: 175 QTAIADFLDRETGRIDSLMAKKRQLIALLKEKRCALISHIVTRGLPEAAADEFGLKPHTR 234

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
            K+S IEW+G VP+ W VK  +    E   +N +L + N     +G    K E       
Sbjct: 235 FKNSDIEWLGQVPEGWGVKKVW---IERVSRNIELQDGN-----HGEQHPKAEDYVGEGI 286

Query: 277 PESYETYQIVDPGEIVFRFIDL--QNDKRSLR-------SAQVMERGIITSAYMAVKPH- 326
           P  +     +D G+I F   +   +    SLR          +  +G I    +  K H 
Sbjct: 287 P--FVMANHIDNGKIDFNKCNYIEKEQADSLRIGFSNEGDVLLTHKGTIGRVGIVQKSHF 344

Query: 327 ----------------GIDSTYLAWLMRS---YDLCKVFYAMGSGLRQSLKFEDVKRLPV 367
                            I + +L WLM+S    D  K+   +GS  R  +   D K L  
Sbjct: 345 PYVMLTPQVTYYRCLREIQNRFLFWLMQSKFWQDQLKLLAGLGS-TRAYIGLLDQKTLSF 403

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           L+P  KEQF I   ++ ET+++D LVEK++  I  L+E R++ I AAVTG+ID+R
Sbjct: 404 LIPSEKEQFAIATYLDRETSKLDRLVEKVDAVIARLQEYRTALITAAVTGKIDVR 458


>gi|227540803|ref|ZP_03970852.1| type I restriction-modification system S subunit [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227183432|gb|EEI64404.1| type I restriction-modification system S subunit [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 442

 Score =  158 bits (399), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 121/446 (27%), Positives = 204/446 (45%), Gaps = 33/446 (7%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT---- 60
           + Y  YKDSGV WI  IP+ W V       K + G   +  +D+   G+  +  G     
Sbjct: 2   EVYEHYKDSGVPWIDKIPQLWTVDRFSMSFKFSRGLDIKK-RDLEAAGIPVLSYGQIHAK 60

Query: 61  -----------GKYLPKD--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGIC 107
                       +++P D  G     D        +G +++      +  A   +F    
Sbjct: 61  HNPVVTISPDLVRFIPADKIGGGNLEDAR----LREGDLVFADTSEDVHGA--GNFSRSD 114

Query: 108 STQF-------LVLQPKDVLPELLQGWLLSIDV-TQRIEAICEGATMSHADWKGIGNIPM 159
            +Q        L+ +P++        +L S +    +I    +G  +         +  +
Sbjct: 115 GSQMIHAGYHTLLARPRETYEHKYFAYLFSSEAWRHQIRRAVQGVKVYSITQGVFKHAQL 174

Query: 160 PIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKD 219
             PP+  Q  I   + A+T  ID ++ +  R   LL+  K+ L+++ VTKGLNP+  MKD
Sbjct: 175 LRPPVETQDAIVAFLDAKTAEIDVVVEKLRRQRALLERYKRELIAHTVTKGLNPESPMKD 234

Query: 220 SGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPES 279
           S  E++G  P  W+ +P F +  ++   N++L     L    G+II K +  +     + 
Sbjct: 235 SEYEFIGTYPADWQNRPLFDICDQVKLDNSELQTIVALQFKNGSIIAKPDWDDSPQSLDI 294

Query: 280 YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH-GIDSTYLAWLMR 338
              Y +V PG IV   ++L  D ++ R   V   G ITSAY+ + PH  I+S YL +L +
Sbjct: 295 LSGYTLVSPGMIVINGLNLNYDFKTKRIGLVKNNGAITSAYIVISPHRDIESRYLNYLFK 354

Query: 339 SYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
           S D  K  + M  G+R+ L ++D++RL + +P   +Q  I N ++ +TA ID L+  I++
Sbjct: 355 SIDAQKALHGMTEGVRKILNWKDIRRLTLPMPNSSQQIAIANYLDTKTAEIDSLIANIDR 414

Query: 399 SIVLLKERRSSFIAAAVTGQIDLRGE 424
            I LL   R   I   VTG++ +  E
Sbjct: 415 QIALLGAYRKQVINDVVTGKVRVSEE 440


>gi|167917951|ref|ZP_02505042.1| probable type I restriction-modification system [Burkholderia
           pseudomallei BCC215]
          Length = 442

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 131/447 (29%), Positives = 210/447 (46%), Gaps = 44/447 (9%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY--L 64
           YPQYKDSG  W+G +P  W VV  +R          E  +D    G E + S + KY  +
Sbjct: 6   YPQYKDSGASWLGRVPTSWAVVQARRLF--------EQRRDAALPGDEQL-SASQKYGVV 56

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGP---------YLRKAIIADFDGICSTQFLVLQ 115
           P+       D   V +   G   +  + P         +      + F G  S  + VL+
Sbjct: 57  PQRLFMELEDQKVV-LALSGLENFKHVEPNDFVISLRSFQGGIEHSAFGGCVSPAYTVLR 115

Query: 116 PKDVLPELLQGWLLSID-----VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
               +      +LL  D     +    + I +G  +S+  +   G + +P+P + EQ  I
Sbjct: 116 ATSKIAPDFWAYLLKSDTYISALQTVTDGIRDGKNISYMQF---GALCVPVPNIDEQSAI 172

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              +  ET +ID LI E+ + I LL EK+QA +SY VT+GLNPD  MKDSG+ W+G VP 
Sbjct: 173 AAFLDCETGKIDALIAEQEKLIALLAEKRQAALSYAVTRGLNPDAPMKDSGVAWLGEVPA 232

Query: 231 HW---EVKPFFALVTE--------LNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPES 279
           HW    VK     +T         ++ + +  ++S  L+   G   +  +  ++    E+
Sbjct: 233 HWVIRRVKSVSVFMTSGPRGWSERISDEGSIFVQSGDLNDFLGVEFEIAKRVSVEFDAEA 292

Query: 280 YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH-GIDSTYLAWLMR 338
             T   +  G++V      +  K ++  A V E   +      ++P   +   +L   ++
Sbjct: 293 ERTR--LANGDVVVCITGAKTGKVAV-CASVPEPAYVNQHLCLIRPSPDVLPLFLGNSLK 349

Query: 339 SYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
           S      F     GL+Q L  ++V+   +++PP  EQ +I   I+ ETAR+D L  +  +
Sbjct: 350 STIGQTQFELSQYGLKQGLSLDNVREALIVLPPPGEQVEIVTFIDAETARLDELKAEAAR 409

Query: 399 SIVLLKERRSSFIAAAVTGQIDLRGES 425
           +I LLKERRS+ IAAAVTG+ID+R  +
Sbjct: 410 AIELLKERRSALIAAAVTGKIDVRNAA 436


>gi|126462620|ref|YP_001043734.1| restriction modification system DNA specificity subunit
           [Rhodobacter sphaeroides ATCC 17029]
 gi|126104284|gb|ABN76962.1| restriction modification system DNA specificity domain [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 456

 Score =  156 bits (395), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 131/454 (28%), Positives = 215/454 (47%), Gaps = 49/454 (10%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTGR--TSESGKDIIYIGLEDVESGT- 60
           + YP YKDSGV+W+G +P+ W+V  ++    +L TG   +    +D +  G+  V     
Sbjct: 2   RRYPAYKDSGVEWLGEVPEGWEVKCLRMIADELQTGPFGSQLHTEDYVTAGVPIVNPSNI 61

Query: 61  --GKYLPKDGNSRQSDTS---TVSIFAKGQILYGKLGPYLRKAIIAD--FDGICSTQFLV 113
             G+ +P D       T+          G I+ G+ G   R A++ D     +C T  L 
Sbjct: 62  LDGQIVPDDEIGVDEATALRLANHALLPGDIILGRRGELGRCAVVPDGTMPLLCGTGSLR 121

Query: 114 --LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
             L+    LP+ +   + +  V + +     G+TM + +   +G I + +P L EQ  I 
Sbjct: 122 IRLKSSQALPDFIAECIRTPRVREWLSLQSVGSTMDNLNTAIVGKIQIALPSLPEQRAIT 181

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
             +  ET +ID L+ E+ R I LL EK+QA++++ VT+GLNPD  +K SGI+W+G +P+ 
Sbjct: 182 AFLNRETAKIDALVEEQRRLIALLAEKRQAVLNHAVTRGLNPDALLKPSGIDWLGDIPEG 241

Query: 232 WEVKPFFALVTELNRKNTK-------LIESNILSLSYGNIIQKLETRNMGLKPESYETYQ 284
           WEV P    V  L   +T         ++ +I   S  +I Q    R   +    YET +
Sbjct: 242 WEVVPIRK-VARLESGHTPSRSRPEWWVDCHIPWFSLADIWQVRPGRVEYV----YETAE 296

Query: 285 IVDPGEIVFRFIDLQNDK-RSLRSAQVMERGIITSAYMAVKPHGIDST------------ 331
            V         + LQN   R L +  VM     +  + AV    + +T            
Sbjct: 297 AVSE-------LGLQNSSARLLPAGTVMLSRTASVGFSAVMGIAMATTQDFANWVCGCRL 349

Query: 332 ---YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
              YL + +R          MGS    ++   D++ L + +PP++EQ  I + +      
Sbjct: 350 LPDYLLYCLRGMPSEFERLKMGS-THNTIYMPDIRTLTIPLPPLEEQKAIVDHVRASVGA 408

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           +D L++    +I LL+ERR++ I+AAVTG+ID+R
Sbjct: 409 LDELMDTATTAITLLQERRAALISAAVTGKIDVR 442


>gi|77361017|ref|YP_340592.1| type I restriction-modification system, S subunit
           [Pseudoalteromonas haloplanktis TAC125]
 gi|76875928|emb|CAI87149.1| putative type I restriction-modification system, S subunit
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 442

 Score =  156 bits (395), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 128/450 (28%), Positives = 225/450 (50%), Gaps = 52/450 (11%)

Query: 2   KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTG 61
           + YKAYP+Y++S + W+  IP +W+ +P++       G   +S  D    G+  V++   
Sbjct: 9   RKYKAYPEYQNSDIDWLRKIPNYWQTIPLRLILDTRKGVAFKSN-DFTSSGIRVVKASDI 67

Query: 62  KYLPKDGNSRQSDTSTVSIFAK-----GQILYGKLG--PYLRKAIIAD-------FDG-I 106
           K L  + +     T+ +SI+ K     G I+   +G  P ++ + +          DG +
Sbjct: 68  KKLTINSSEVYLPTNYISIYPKAILRKGDIILSTVGSNPDVKNSAVGQIGVVPEHLDGAL 127

Query: 107 CSTQFLVLQPKD--VLPELL------QGWLLSIDVTQRIEAICEGATMSHADWKGIGNIP 158
            +   +V +PK+  +  E L       G+   +D+          +++S +D   + N  
Sbjct: 128 LNQNTVVFEPKEDKIHREFLFKVIQMNGYRDHLDLNAH--GTANQSSLSISD---MLNFY 182

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           +PIPP  EQ  I   +  ET +IDTLI ++ + IELLKEK+QA++S+ VTKGLNP+  M+
Sbjct: 183 IPIPPKNEQQKIASFLDHETAKIDTLIAKQEKLIELLKEKRQAVISHAVTKGLNPNAPMR 242

Query: 219 DSGIEWVGLVPDHWEVKPFFALVTELNRK--NTKLIESNILSLSYGNIIQKLETRNMGLK 276
           DSG+EW+G VP+HW +      V+  + +  ++ L+E N   L    +I           
Sbjct: 243 DSGVEWLGEVPEHWLIGSLRWKVSISSGEGLSSNLVEKNKTELKKIPVIGGNGVMGFSES 302

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWL 336
             +++T   +     +   + L N       + + +  +  S++      G D  YL  L
Sbjct: 303 SNTHKTAIAIGRVGALCGNVHLIN-----YISWITDNALKISSW-----DGFDENYLISL 352

Query: 337 MRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
           +++ +L  +       L   +  E +K L V++PP+KEQ      IN++  +I  L +K+
Sbjct: 353 LKAANLNNLASTTAQPL---ITGEQIKSLIVVIPPLKEQIK----INLKLTKIVNLFDKL 405

Query: 397 EQ----SIVLLKERRSSFIAAAVTGQIDLR 422
           E+     I LLKER+++ I+AAVTG+ID+R
Sbjct: 406 EKRSKDGINLLKERKTALISAAVTGKIDVR 435


>gi|332974851|gb|EGK11766.1| restriction modification system DNA specificity subunit
           [Psychrobacter sp. 1501(2011)]
          Length = 442

 Score =  156 bits (395), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 133/448 (29%), Positives = 216/448 (48%), Gaps = 52/448 (11%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTK--------LNTGRTSESGKDIIYIGLED 55
           YKAYP+YKDSGV+WIG IP  W++  IK  +K        LN     E   ++ Y G   
Sbjct: 12  YKAYPEYKDSGVEWIGEIPSGWELTRIKYVSKCLDGARIPLNASERGEMSGNVPYWGANK 71

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLG-PYLRKAIIADFDGIC----STQ 110
           V      YL                F +  +L G+ G P+  K     F+       +  
Sbjct: 72  VVDHINDYL----------------FDEELVLLGEDGAPFFDKNKDVAFNVSGKIWPNNH 115

Query: 111 FLVLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
             VL+P  + V P  L+  L   D    I     G+T    +   +  I +  P L EQ 
Sbjct: 116 VHVLRPLMEKVEPRFLKHSLNCADFYLYIS----GSTRDKLNQSDMNEIFIRAPKLIEQK 171

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I   +  ET +ID LI ++ R IELL EK+QA++S+ VTKGLNPD  MKDSG+EW+G V
Sbjct: 172 QIANFLDYETAKIDNLIEKQQRLIELLTEKRQAVISHAVTKGLNPDAPMKDSGVEWLGDV 231

Query: 229 PDHWEVKPF--FALVTE-LNRKNTKLIESNILSLSYGNIIQ---KLETRNMGLKPESY-E 281
           P+HW V      A + E    ++ +     I  +S  NI +           +  E Y +
Sbjct: 232 PEHWIVTKLRQLAFLQEGPGLRHWQFKAQGIKVISVTNITEAGIDFTRLEKFISHEEYLQ 291

Query: 282 TYQ--IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM---AVKPHGIDSTYLAWL 336
           +YQ   V+ G+I+       N    + + +  ++ I+ ++ +    +K   +   ++ + 
Sbjct: 292 SYQHFTVNKGDILLS--SSGNSWGKVATYEGDDKVILNTSTIRLNELKHRPLVQPFIKFF 349

Query: 337 MRSYDLCK--VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           + S + C+  +  AM    + +     +  +  +VPP+ EQ+ I+  I+ + ++I  L++
Sbjct: 350 LLS-EACREQLGLAMTGSCQPNFGPTHLNEVKTVVPPVDEQYAISKYIDEKVSKISELLQ 408

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLR 422
             E +I L++ERR++ I+AAVTG+ID+R
Sbjct: 409 VCESTIQLMQERRTALISAAVTGKIDVR 436


>gi|325981608|ref|YP_004294010.1| restriction modification system DNA specificity domain
           [Nitrosomonas sp. AL212]
 gi|325531127|gb|ADZ25848.1| restriction modification system DNA specificity domain
           [Nitrosomonas sp. AL212]
          Length = 467

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 126/467 (26%), Positives = 217/467 (46%), Gaps = 66/467 (14%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIK--RFTKLNTGRTSESGKDIIYIGLEDVESGTG 61
           Y+AYP+YK+SGV+WIG  P +W +  +K   + K   G      +D          +  G
Sbjct: 12  YQAYPEYKNSGVEWIGEYPLNWNLTRVKFESYVKARVGWHGLKSEDF---------TDEG 62

Query: 62  KYLPKDGNSR---------------QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG- 105
            +L    + R               + +         G +L  K G   + A+++   G 
Sbjct: 63  PFLITGSDFRGPVINWNECYHCDLARYEQDPYIQLKDGDLLITKDGTIGKVALVSGLAGK 122

Query: 106 --ICSTQFLVLQPKDVLPELLQGWLLSIDV-TQRIEAICEGATMSHADWKGIGNIPMPIP 162
             + S  F+V    +        WLL   V T  ++    G+T+ H       N    IP
Sbjct: 123 ATLNSGVFVVRPLTNNYTSRFYFWLLQASVFTGFVDFNKTGSTIVHLYQDTFVNFKYAIP 182

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
              EQ+ I   +  ET +IDTLI ++ + I+LLKEK+QA++S+ VTKGLNP+ KM+DSG+
Sbjct: 183 SFNEQLTIANFLDHETAKIDTLIEKQQQLIKLLKEKRQAVISHAVTKGLNPNAKMRDSGV 242

Query: 223 EWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL------- 275
           EW+G VP+HW +K     V E +R        + ++  +G+ +  LE +++G+       
Sbjct: 243 EWLGEVPEHWSMKIKLVSVAEGSR-------GSFVNGPFGSDLLSLELQDVGVPVIYIRD 295

Query: 276 -----------------KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITS 318
                            K    E  ++V    ++ +  D   +  +    +     IIT 
Sbjct: 296 LKQTGYMRKSAVCVTEEKARQLEICKVVSGDVLIAKVGDPPGE--ACIYPENEPAAIITQ 353

Query: 319 AYMAVKPH-GIDSTYLAWLMRSYDLCKVFYAMGS--GLRQSLKFEDVKRLPVLVPPIKEQ 375
             + ++ + G+ + Y   ++ + DL KV     S    R+ +   D K++  ++P + EQ
Sbjct: 354 DVIRIRVNRGVINPYYLVMLLNSDLGKVVVDNISIESTRKRISLGDFKQVRFIIPSLSEQ 413

Query: 376 FDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            DI + + +   +ID L+ K +  + L+ ERR++ I+AAVTG+ID+R
Sbjct: 414 SDIVSFVELRCRKIDTLIAKAQSMVSLIIERRTALISAAVTGKIDVR 460


>gi|21229080|ref|NP_635002.1| type I restriction-modification system specificity subunit
           [Methanosarcina mazei Go1]
 gi|20907634|gb|AAM32674.1| type I restriction-modification system specificity subunit
           [Methanosarcina mazei Go1]
          Length = 460

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 121/430 (28%), Positives = 206/430 (47%), Gaps = 23/430 (5%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K YP YKDSGV W+G +P+HWK   +KR   +   R+ +   D   +     +    K L
Sbjct: 6   KPYPAYKDSGVPWLGEVPEHWK---LKRTKTVLRERSQKGFPDEPLLAATQTKGVVRKEL 62

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELL 124
            ++          +    +       L  +      A   GI S  + +L P +      
Sbjct: 63  YENRTVLALKDLHLLKLVRVNDFVISLRSFQGGIEFAHEQGIISPAYTILYPVEAQNHGF 122

Query: 125 QGWLLSI-----DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
             WL        +++  +  I EG  +   D+  +    +P+PP +EQ  I   +     
Sbjct: 123 LAWLFKSKPYIENLSLFVTGIREGQNI---DYVKLSRSELPLPPFSEQSSIVRYLDHIDR 179

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
           RI   I  + +FI+LL+E+KQA++   VT GL+P+VK+K SG+EW+G VP+HWEVKP   
Sbjct: 180 RIRRYIHAKQKFIKLLEEQKQAIIHQSVTHGLDPNVKLKPSGLEWLGDVPEHWEVKPAKW 239

Query: 240 LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPGEIVFRFIDL 298
              E++ +++   E  +LS+S+   +     +N+ +   ESY  Y++    ++V     +
Sbjct: 240 YYHEIDERSSTGSE-ELLSVSHITGVTPRSEKNITMFMAESYVGYKLCRENDLVIN--TM 296

Query: 299 QNDKRSLRSAQVMERGIITSAYMAVKP---HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQ 355
                +L  AQ  + GI++ +Y   +P       S Y+  L+R+      +    +G+  
Sbjct: 297 WAWMAALGVAQ--QTGIVSYSYGVYRPIHKEAFLSQYIDLLLRTKPYVAEYICRSTGIHS 354

Query: 356 S---LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIA 412
           S   L  E   R+P++ PPI EQ  I + I+ +T+ ++  +    Q I LL+E R+  IA
Sbjct: 355 SRLRLYPEQFLRIPIIRPPIVEQQAILDEIHNKTSELEHAINTSNQEISLLREYRTRLIA 414

Query: 413 AAVTGQIDLR 422
             VTG++D+R
Sbjct: 415 DVVTGKLDVR 424



 Score = 69.3 bits (168), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 105/220 (47%), Gaps = 20/220 (9%)

Query: 210 GLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLE 269
            L P    KDSG+ W+G VP+HW++K          R  T L E +        ++   +
Sbjct: 4   NLKPYPAYKDSGVPWLGEVPEHWKLK----------RTKTVLRERSQKGFPDEPLLAATQ 53

Query: 270 TRNMGLKPESYETYQIVDPGEI-VFRFIDLQNDKRSLRSAQ-----VMERGIITSAYMAV 323
           T+ + ++ E YE   ++   ++ + + + + +   SLRS Q       E+GII+ AY  +
Sbjct: 54  TKGV-VRKELYENRTVLALKDLHLLKLVRVNDFVISLRSFQGGIEFAHEQGIISPAYTIL 112

Query: 324 KP-HGIDSTYLAWLMRSYDLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITN 380
            P    +  +LAWL +S    +      +G+R  Q++ +  + R  + +PP  EQ  I  
Sbjct: 113 YPVEAQNHGFLAWLFKSKPYIENLSLFVTGIREGQNIDYVKLSRSELPLPPFSEQSSIVR 172

Query: 381 VINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            ++    RI   +   ++ I LL+E++ + I  +VT  +D
Sbjct: 173 YLDHIDRRIRRYIHAKQKFIKLLEEQKQAIIHQSVTHGLD 212


>gi|71900230|ref|ZP_00682368.1| similar to Restriction endonuclease S subunits [Xylella fastidiosa
           Ann-1]
 gi|71730003|gb|EAO32096.1| similar to Restriction endonuclease S subunits [Xylella fastidiosa
           Ann-1]
          Length = 307

 Score =  154 bits (389), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 87/238 (36%), Positives = 131/238 (55%), Gaps = 4/238 (1%)

Query: 14  GVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQS 73
           G++W+  +P HW+V  +K   +  + +++   +D IY+ LE V+S TG   P  G    +
Sbjct: 27  GIEWLQDVPGHWEVQRLKFIARNMSEQSTVKARDEIYLALEHVQSWTGVARPLKGTVEFA 86

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLLSI 131
             STV  F    IL+GKL PYL K   A+  G+C ++FLVL+P+   +LP  L+  L   
Sbjct: 87  --STVKRFFADDILFGKLRPYLAKVTRANCVGVCVSEFLVLRPRKELILPSYLEHLLRCK 144

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
            V   I +   GA M   DW  IGN+ +P+PPL EQ  I   + A+ V I   I  +   
Sbjct: 145 RVIDLINSATAGAKMPRVDWAFIGNVRLPLPPLPEQKQIAAYLRAQDVHIARFIKVKRDL 204

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT 249
           I+LL E+K  ++ + VT+GL+  V +K SGIEW+G VP HW+       V+ ++   T
Sbjct: 205 IKLLTEQKLRIIDHAVTRGLDASVALKPSGIEWLGDVPVHWDTSRLKYCVSRIHAGGT 262


>gi|288986940|ref|YP_003456903.1| restriction modification system DNA specificity domain protein
           [Allochromatium vinosum DSM 180]
 gi|288898319|gb|ADC64153.1| restriction modification system DNA specificity domain protein
           [Allochromatium vinosum DSM 180]
          Length = 453

 Score =  153 bits (387), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 131/454 (28%), Positives = 222/454 (48%), Gaps = 44/454 (9%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGR---TSESGKDII-YIGLEDVESG 59
           +  Y +YKDSGV+W+G +P+HW +  +K   +           +G+D+I  I + D +  
Sbjct: 3   FPRYERYKDSGVEWLGEVPEHWILDRLKWSVEGCINGLWGDDPNGEDVIPCIRVADFDRA 62

Query: 60  TGKYLPKDGNSRQ--SDTSTVSIFAKGQILYGKLGPYLRK--AIIADFD----GICSTQF 111
             +   +D   R    +         G +L  K G    +   ++  FD     +CS  F
Sbjct: 63  KNRVRAEDLTYRSISEEKRLNRSLKNGDLLIEKSGGGDNQPVGVVVLFDHNLNAVCSN-F 121

Query: 112 LVLQP--KDVLPELLQGWLLSIDVTQRI--EAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
           +   P   +  P  L  +L S+    R+  ++I +   + + D     +    IP + EQ
Sbjct: 122 VARMPVRSNFSPRFL-CYLHSVLYALRLNTKSIKQNTGIQNLDSASYLDERFGIPTVYEQ 180

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
            LI + +  ET +ID LI E+ R +ELLKEK+QA++S+ VTKGLNPD  MKDSGIEW+G 
Sbjct: 181 GLIADFLDRETAKIDALIAEQQRLVELLKEKRQAVISHAVTKGLNPDAPMKDSGIEWLGE 240

Query: 228 VPDHWEVKPFFALVTE---------LNRKNTKLIESNILSLSYGNI-IQKLETRNMGLKP 277
           VP+HW + P   L            L   N   +++ +  +  G++   +L    +    
Sbjct: 241 VPEHWVIVPLKHLTAPGRDIMYGIVLPGPN---VDNGVPIVKGGDVRPHRLRLELLNRTT 297

Query: 278 ESYE---TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLA 334
           E+ E       + P +IV+       D   L   ++++  I            ++S +L 
Sbjct: 298 EAIEAPYARARLRPSDIVYSIRGSIGDA-ELVPDELLDANITQDVARISPDQTVNSLWLL 356

Query: 335 WLMRSYDLCKVFY-----AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           ++M+S    +VF      ++G+ +R  +   D+KR  +  P I+EQ  I   ++ ET ++
Sbjct: 357 FVMKS---VRVFVQLEQRSLGAAVR-GINIFDLKRARIPFPDIQEQKTIATFLDRETTKL 412

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           D L  + + +I LL+ERR++ I+AAVTG+ID+RG
Sbjct: 413 DALTAEAQTAITLLQERRTALISAAVTGKIDVRG 446


>gi|283954324|ref|ZP_06371845.1| hypothetical protein C414_000210006 [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283794123|gb|EFC32871.1| hypothetical protein C414_000210006 [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 411

 Score =  153 bits (386), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 119/428 (27%), Positives = 215/428 (50%), Gaps = 34/428 (7%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKD 67
            +KDSG++W+G IP+ W+VVPI+  F + N  R +++   ++ + +       G     D
Sbjct: 3   NFKDSGIEWLGEIPQDWEVVPIRCCFGEFNI-RCNDNDYPLLSVTI-----ANGVVYQND 56

Query: 68  GNSRQS----DTSTVSIFAKGQILYGKLGPYLRKAIIADFD-GICSTQFLVLQPKDVLPE 122
              ++     D S   I   G I Y K+  +     I   + GI S  ++V  P   +  
Sbjct: 57  ITDKKDISNDDKSNYKIVPLGAIAYNKMRMWQGAVGINMLEKGIVSPAYVVAIPNKQINI 116

Query: 123 LLQGWLL-SIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
               +LL S ++    E    G  + M++  ++   NI +P+PPL EQ  I   +  +  
Sbjct: 117 SFSYYLLKSRNIIGEYEKNSYGLCSDMNNLRYEDFQNIKIPLPPLKEQEQIVNFLDEKCE 176

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
           +I   I ++ + I LLKE+KQAL++  +TKGLN +V  KDSGIEW+G +P+HW++     
Sbjct: 177 QIANFIEKKEKLISLLKEQKQALINETITKGLNKNVNFKDSGIEWLGEIPEHWKILKLKH 236

Query: 240 LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQI----VDPGEIVFRF 295
           + +  N+K      SN +    G  ++ +E++     P S   ++      + G+I+F  
Sbjct: 237 IASLRNQK------SNNIDFRIG--LENIESKTGKFIPSSEIVFEEDGIGFEKGDILFGK 288

Query: 296 IDLQNDKRSLRSAQVMER-GIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLR 354
           +     +  L    + +R GI  S ++ +K     + ++ +LM S     +  +   G +
Sbjct: 289 L-----RPYLAKVFLTDRDGICVSEFLVLKIKSESNKFIKFLMLSSLFIDIVDSSTYGTK 343

Query: 355 Q-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAA 413
                +E +  L + +PP+KEQ  I N ++ +  +ID+L+EK ++ I L+KE +++ I  
Sbjct: 344 MPRANWEFIGNLKIPLPPLKEQEQIANFLDKKCEKIDLLIEKTKKQIKLIKEYKTTLINQ 403

Query: 414 AVTGQIDL 421
           AV G++DL
Sbjct: 404 AVCGRMDL 411


>gi|110639314|ref|YP_679523.1| type I restriction-modification system [Cytophaga hutchinsonii ATCC
           33406]
 gi|110281995|gb|ABG60181.1| probable type I restriction-modification system [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 432

 Score =  152 bits (385), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 127/440 (28%), Positives = 207/440 (47%), Gaps = 37/440 (8%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + YP YKDSGV+W+G IPKHW+ + +K   +  + +  ++ +      L  V    G  +
Sbjct: 6   QKYPAYKDSGVEWLGEIPKHWECIRMKHLFRDYSEKNKQNEE------LLSVTQNQG-VV 58

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRK----AIIADFDGICSTQFLVLQPKDVL 120
           P+     +    + ++ +   I  G     LR           DGI S  + VL+ K  +
Sbjct: 59  PRSWVESRMVMPSGALESFKFIQKGDFAISLRSFEGGLEYCHHDGIISPAYTVLKTKRKI 118

Query: 121 PELLQGWLLSI-----DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
                 +L        ++   I  I EG  +S+ +   +    +PIP + EQ  I   + 
Sbjct: 119 ANQYYKYLFKSSAFISELQTSIVGIREGKNISYPE---LSYSLLPIPKIDEQSCIATFLD 175

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            +T +ID  I+ + + IELLKE++Q L+   VT+GLNP VKMKDSG+EW+G VP+ WEVK
Sbjct: 176 DKTAKIDQAISIKQKQIELLKERRQILIHKAVTRGLNPKVKMKDSGVEWIGEVPEGWEVK 235

Query: 236 PFFALVTELNRKNTKLIESNIL------SLSYGNIIQKLETR---NMGLKPESYETYQIV 286
               L   + R N+   + ++L      +L YG   +  E     N  +  E Y+  QIV
Sbjct: 236 KLLGLCNFI-RGNSSFGKDDLLNDGEYVALQYGKTYKVNEVNEEYNYFVNNEFYKASQIV 294

Query: 287 DPGEIVFRFIDLQNDKRSLRSAQVMER---GIITSAYMAVKPHG--IDSTYLAWLMRSYD 341
           + G+ +   I        L      +R   G+I    + + P+   I+S YL +  R + 
Sbjct: 295 NYGDTI--IIATSETIEELGHTAYYKRNDLGLIGGEQILLNPNNDKINSHYLYFTSRVFS 352

Query: 342 LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
                YA G  + +     D+K + + +PP+ EQ  I   I   TA+I   +   E  I 
Sbjct: 353 KELRKYATGIKVFR-FNINDLKTIYIAIPPLSEQQQIVEYIETTTAKIATAISLKENEIE 411

Query: 402 LLKERRSSFIAAAVTGQIDL 421
            LKE +++ + +AVTG+I +
Sbjct: 412 KLKEYKANLVNSAVTGKIKV 431


>gi|226940441|ref|YP_002795515.1| Type I restriction-modification system, S subunit [Laribacter
           hongkongensis HLHK9]
 gi|226715368|gb|ACO74506.1| Type I restriction-modification system, S subunit [Laribacter
           hongkongensis HLHK9]
          Length = 453

 Score =  152 bits (385), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 139/458 (30%), Positives = 203/458 (44%), Gaps = 64/458 (13%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG-----LEDVESGTG 61
           YP YKDSGV+W+ +IP HW+VV +K   ++      E G  ++ I      ++D+ES  G
Sbjct: 6   YPAYKDSGVEWLRSIPSHWEVVRLKNIFEIRKRIAGELGHSVLSITQRGIKVKDIESNDG 65

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ---FLVLQPKD 118
           +           D S   I   G      +        I+   G+ S     F +L    
Sbjct: 66  QI--------SMDYSKYQIVLPGDFAMNHMDLLTGYVDISSTHGVTSPDYRVFAMLDNAH 117

Query: 119 VLPELLQGWLLSIDVTQRI-EAICEGATMSHADWK----GIGNIPMPIPPLAEQVLIREK 173
            +P      L      Q+I  A  +GA+     W+       N  +P PP  EQ  I   
Sbjct: 118 CVPRYFLH-LFQNGYRQKIFYAFGQGAS-EFGRWRFPTDQFNNFRLPCPPDDEQAAIATF 175

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  ET +ID LI E+ + I LL EK+QA +S+ VT+GL+P V MKDSG+EW+G VP HW 
Sbjct: 176 LDRETAKIDALIAEQEKLIALLAEKRQATISHAVTRGLDPAVPMKDSGVEWLGQVPAHW- 234

Query: 234 VKPFFALVTELNRKNTKLIESNILSLSYGNIIQ-------KLETRNMGL-KPESYETY-Q 284
                 ++  + RK  K IE       +    +       K    N G+ +PE  +    
Sbjct: 235 ------VICSVRRK-LKRIEQGWSPECFSRPAEAGEWGVLKAGCVNGGIFRPEENKALPD 287

Query: 285 IVDPGE-IVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDL 342
            + P E I+ +  DL   + S   A V      + AY++  P H + S  +  L      
Sbjct: 288 TLAPDENILIKDGDLLMSRASGSPALVG-----SVAYLSAPPAHLMLSDKIFRLHLEQGT 342

Query: 343 CKVFYAM-----------------GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
              F A+                   GL  +L    +K   + +PP  EQ +I      E
Sbjct: 343 LPQFVAIAFGARYLRHQIEQAISGAEGLANNLPQTSLKGFTIAIPPEVEQQEIVVFTQQE 402

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           TA++D L    E ++ LLKERR++ IAAAVTGQID+RG
Sbjct: 403 TAKLDALKIAAEHAVSLLKERRAALIAAAVTGQIDVRG 440


>gi|258513230|ref|YP_003189486.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-01]
 gi|256635133|dbj|BAI01107.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-01]
 gi|256638188|dbj|BAI04155.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-03]
 gi|256641242|dbj|BAI07202.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-07]
 gi|256644297|dbj|BAI10250.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-22]
 gi|256647352|dbj|BAI13298.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-26]
 gi|256650405|dbj|BAI16344.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-32]
 gi|256653396|dbj|BAI19328.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-01-42C]
 gi|256656449|dbj|BAI22374.1| type I DNA specificity S subunit [Acetobacter pasteurianus IFO
           3283-12]
          Length = 420

 Score =  152 bits (384), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 116/429 (27%), Positives = 195/429 (45%), Gaps = 30/429 (6%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           Y  Y  Y+DSGVQW+G  P +W++  +    +    + S++         E +       
Sbjct: 6   YSKYDAYRDSGVQWVGQFPANWELARLGGLFEERRHKVSDTD-------FEPLSVTKNGI 58

Query: 64  LPKDGNS-RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
            P+  N+ + +D     +   G  +          + I+  DG  S   +VL+PK +LPE
Sbjct: 59  FPQLANAAKTNDGENRKLVRAGDFVINSRSDRKGSSGISPLDGSVSLINIVLEPKRILPE 118

Query: 123 LLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
                L S    +    +  G  A +    +  +  I + +P   EQ  I   +  +   
Sbjct: 119 FCHHLLKSYAFVEEYYRVGRGIVADLWTTRYDEMRTILIALPSPDEQRTIAAFLDGKCAL 178

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID  +  + + I LL E++Q L+   VT+GLNPD  MKDSGI+W+G +P HWEVK    +
Sbjct: 179 IDEAVRIKEKQIRLLVERRQILIQQAVTRGLNPDAPMKDSGIDWIGQIPAHWEVKRNKHM 238

Query: 241 VTELNRKNTKLIESNI-----LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
             E+N ++ K  E ++     L L   ++++K       L  ESY+  ++V  G++V   
Sbjct: 239 FVEINERSAKGEEQHLSMSQKLGLVPADLVEK------SLASESYQGAKLVRTGDLVLNR 292

Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAVKP--HGIDSTYLAWLMRSYDLCKVFYAMGSGL 353
           +       ++ S   ME G+++  Y   +P   G  S Y   L ++      F     G+
Sbjct: 293 LKAH---LAVFSLAPME-GLVSPDYSVFRPLVQGASSDYFEILFKTSKYLGEFRLRVRGI 348

Query: 354 RQS---LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
            +    L  +D    P+L+PP+ EQ  I   +   TA+   ++   E  I  L+E ++S 
Sbjct: 349 VEGFYRLYTDDFMDCPLLLPPLDEQLQIVEHVRATTAQFHNVIAIKESQITALREYKTSL 408

Query: 411 IAAAVTGQI 419
           I AAVTG+I
Sbjct: 409 INAAVTGKI 417


>gi|119896299|ref|YP_931512.1| Type I site-specific deoxyribonuclease [Azoarcus sp. BH72]
 gi|119668712|emb|CAL92625.1| Type I site-specific deoxyribonuclease [Azoarcus sp. BH72]
          Length = 449

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 128/445 (28%), Positives = 195/445 (43%), Gaps = 30/445 (6%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTS------ESGKDII-YIGLEDVESG 59
           Y +YKDSGV  +  IP HW+  P+KR   L     S       +G D +  +    V SG
Sbjct: 6   YAEYKDSGVALLATIPAHWEPSPLKRVVALVESGVSVNAVDEPAGPDAVGVLKTSCVYSG 65

Query: 60  TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLG-PYLRKA---IIADFDGI-CSTQFLVL 114
              +        +           G ++  ++  P L  A   +  + D +    +   +
Sbjct: 66  NFSHGENKAVVAEELDRVACPVRAGTLIVSRMNTPALVGAAGLVEENADNLFLPDRLWQV 125

Query: 115 QPKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
                +P+    W  S     +++  C G  A+M +          MP+PP  EQ  I  
Sbjct: 126 HFSGAVPKFAHYWTASPSYRAQVQMACAGTSASMQNLSQDEFLRFVMPLPPKDEQTAIAA 185

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
            +  ET +ID LI ++ + I LL EK+QA +S+ VT+GLNPD  MKDSG+ W+G VP HW
Sbjct: 186 FLDRETAKIDALIAKQEKLIALLAEKRQATISHAVTRGLNPDAPMKDSGVAWLGEVPAHW 245

Query: 233 EVKPFFALVT-----ELNRKNTKLIESNILSLSYGNI----IQKLET--RNMGLKPESYE 281
            V     L +       +R         I  L  G I    I + E    + GL+     
Sbjct: 246 SVSALSYLASLETGATPDRGEPSYWNGTIPWLKTGEINWAPICEAEEFITDAGLE---NS 302

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYD 341
             +I  PG ++         +  +   ++        A +  +   I      + M +YD
Sbjct: 303 AAKIAKPGTLLMAMYGQGVTRGRVALLEIEATYNQACAAINFRSRIIPEFGRYFFMAAYD 362

Query: 342 LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
             +      S +  S       RLP  VPP+ EQ  +   ++VETA++DVL  + E+ I 
Sbjct: 363 HVRDAGNETSQMNLSAGLISKIRLP--VPPLDEQQAVVRFLDVETAKLDVLGAESERGIT 420

Query: 402 LLKERRSSFIAAAVTGQIDLRGESQ 426
           LLKERRS+ IAAAVTGQID+R  ++
Sbjct: 421 LLKERRSALIAAAVTGQIDVRNTAE 445


>gi|330879482|gb|EGH13631.1| restriction modification system DNA specificity domain protein
           [Pseudomonas syringae pv. morsprunorum str. M302280PT]
          Length = 293

 Score =  151 bits (382), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 100/280 (35%), Positives = 161/280 (57%), Gaps = 17/280 (6%)

Query: 154 IGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNP 213
           I N+ +P+PP++EQ  I   +  ET RID LI E+ R IELLKEK+QA++S+ VTKGL+P
Sbjct: 4   IENLRIPLPPISEQNQIARFLDHETARIDALIEEQQRLIELLKEKRQAVISHAVTKGLDP 63

Query: 214 DVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKL---ET 270
            V MKDSG EW+G VP HWE     A+ +E   K    +    +S+ +G   ++L   E+
Sbjct: 64  TVPMKDSGAEWLGEVPAHWETLRIGAVYSEAADKGLAELPVLRVSIHHGVSDKELSEEES 123

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRS--AQVMERGIITSAYMAVKPHGI 328
                + +  E Y+ V PG++V+      N  R+ +     V+  G+++ AY+  +P   
Sbjct: 124 DRKITRIDDREKYKRVRPGDLVY------NMMRAWQGGFGAVLVNGLVSPAYVVARPKNE 177

Query: 329 D-STYLAWLMRS----YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
           D S Y+  L+R+     ++ K  Y + +  R  L ++  K + +++PP  E+  I   I+
Sbjct: 178 DISRYVEQLLRTGCAVEEMRKNSYGI-TDFRLRLYWDQFKNIVIVIPPEVERLQIMERID 236

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
                 + L  + ++ IV+L+ERRS+ I+AAVTG+ID+RG
Sbjct: 237 SLINESEALKSEADRLIVILQERRSALISAAVTGKIDVRG 276



 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 52/216 (24%), Positives = 94/216 (43%), Gaps = 24/216 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPI---------KRFTKLNTGRTSESGKDIIYIGLEDVESGTG 61
           KDSG +W+G +P HW+ + I         K   +L   R S      I+ G+ D E    
Sbjct: 68  KDSGAEWLGEVPAHWETLRIGAVYSEAADKGLAELPVLRVS------IHHGVSDKELSEE 121

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--- 118
           +   K   +R  D         G ++Y  +  +         +G+ S  ++V +PK+   
Sbjct: 122 ESDRK--ITRIDDREKYKRVRPGDLVYNMMRAWQGGFGAVLVNGLVSPAYVVARPKNEDI 179

Query: 119 --VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
              + +LL+      ++ +    I +     +  W    NI + IPP  E++ I E+I +
Sbjct: 180 SRYVEQLLRTGCAVEEMRKNSYGITDFRLRLY--WDQFKNIVIVIPPEVERLQIMERIDS 237

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLN 212
                + L +E  R I +L+E++ AL+S  VT  ++
Sbjct: 238 LINESEALKSEADRLIVILQERRSALISAAVTGKID 273


>gi|332800154|ref|YP_004461653.1| restriction modification system DNA specificity domain-containing
           protein [Tepidanaerobacter sp. Re1]
 gi|332697889|gb|AEE92346.1| restriction modification system DNA specificity domain protein
           [Tepidanaerobacter sp. Re1]
          Length = 431

 Score =  151 bits (382), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 121/442 (27%), Positives = 208/442 (47%), Gaps = 37/442 (8%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M ++K Y +YKDSG++WIG IP+ WK+  +K    +  G++ +S +         +E G 
Sbjct: 1   MSNFKRYDKYKDSGIEWIGEIPEGWKITKLKYICSITMGQSPKSEE-------YSLEEGG 53

Query: 61  GKYLPKDGNSRQSD--------TSTVSIFAKGQ-ILYGKLGPYLRKAIIADFDGICSTQF 111
             +L   GN+  ++          T + F+K   IL     P  +  I     GI     
Sbjct: 54  LPFL--QGNAEFTELYPQPKIYCDTANKFSKANDILLSVRAPVGKMNISDRVYGIGRGLC 111

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
            +   K  L  L     +S+   + +    +G+T        + N+   +PP  EQ+ I 
Sbjct: 112 AITAQKVHLKYLWYSMNVSL---EELSINSQGSTFEAVTVADVDNLSAIVPPADEQISIA 168

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
             +  +T  ID LI ++ + IELL+EK+QA+++  VTKGLNP+VKMKDSGIEW+G +P+ 
Sbjct: 169 NFLDQKTAEIDDLIADKEKLIELLQEKRQAVITEAVTKGLNPNVKMKDSGIEWIGEIPEG 228

Query: 232 WEVK--PFFALVTELNRKNTKLIESNILSLSYGNIIQKLE---TRNMGLKPESYETYQIV 286
           W V    + AL+ +         +  I  +  G++    E    +++  K       ++V
Sbjct: 229 WRVSKIKYEALINKKTLSENTDDDFEIDYIDIGSVTSVGEINGIQSLSFKDAPSRARRVV 288

Query: 287 DPGEIVFRFIDLQNDKRSLRSAQVMERG----IITSAYMAVKP-HGIDSTYLAWLMRSYD 341
             G  +   +     +  L++   +E      + ++ +  + P   I   YL +LMRS  
Sbjct: 289 SEGNTIVSTV-----RTYLKAIAFIENVHSNLVCSTGFAVLTPLSNIVPKYLFYLMRSEK 343

Query: 342 LCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
                     G+   ++   D+  L  ++P ++EQ +I   ++  + RI+ L  +IE  I
Sbjct: 344 YVNEIVRRSVGVSYPAVNASDIGVLECVLPSVREQINIVEYLDKCSKRINQLTNEIELQI 403

Query: 401 VLLKERRSSFIAAAVTGQIDLR 422
             L+E R S I  AVTG+ID+R
Sbjct: 404 QKLREYRQSLIFEAVTGKIDVR 425


>gi|307244176|ref|ZP_07526291.1| type I restriction modification DNA specificity domain protein
           [Peptostreptococcus stomatis DSM 17678]
 gi|306492326|gb|EFM64364.1| type I restriction modification DNA specificity domain protein
           [Peptostreptococcus stomatis DSM 17678]
          Length = 433

 Score =  151 bits (382), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 126/448 (28%), Positives = 205/448 (45%), Gaps = 51/448 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +YKDSG+ WIG IP+HW V+  K F  L TG +           + D E    KY+ +
Sbjct: 3   YEKYKDSGIDWIGEIPEHWGVIKFKYFADLFTGNS-----------IPDEE----KYMYE 47

Query: 67  DGNSRQSDTSTVSIFAKGQILY--GKLGPYLRK-------------------AIIADF-- 103
              +     +T  ++  G+I Y  G + PY  K                    +   F  
Sbjct: 48  FKENGHPYIATKDVYMDGRINYDNGMIIPYEHKKFKIAPVNSTLMCIEGGSAGVKKSFLE 107

Query: 104 DGIC-STQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
           + +C   +      K+   +    + LS    +R  A+     +   + + + N    IP
Sbjct: 108 EDVCFGNKLCCFNVKEGFNKKYIFYFLSSPDYERYFAMNLNGLIGGVNIQRLKNFEAIIP 167

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
            + EQ  I   +  +T +ID++I E     E L+  K+ L++++VTKGLN +V MKDSG+
Sbjct: 168 SIVEQEKIAAYLDEKTEKIDSIIKELEDQREKLELYKRKLIAHVVTKGLNENVPMKDSGV 227

Query: 223 EWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET 282
           +W+G VP+HW+V+       E+ ++     E  +LS++   I  K   +N G   ESYE 
Sbjct: 228 DWIGAVPEHWKVEK-IKWNFEIVKRQDGREERPVLSITQQGIKIKDIEKNDGQMAESYEK 286

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI---DSTYLAWLMRS 339
           YQ+V+PG+     +DL          +    G+ +  Y   +       D+ Y  +L + 
Sbjct: 287 YQLVEPGDYAMNSMDLLTGWIDCSKYE----GVTSPDYRVFRLKNSELNDNQYFNYLFQM 342

Query: 340 YDLCKVFYAMGSGL----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
               ++FY +G G+    R  L+ E    + + VPP  EQ +I N+I  +  +I  +  K
Sbjct: 343 CYTRRIFYRIGQGVSNLGRWRLQREPFLNMEIPVPPTDEQKEIANLIKEKDLQIRKVDRK 402

Query: 396 IEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           I+  I  L E R S I  AVTG+I + G
Sbjct: 403 IKLQIEKLNEYRKSIIHDAVTGKIKIGG 430


>gi|294054710|ref|YP_003548368.1| restriction modification system DNA specificity domain protein
           [Coraliomargarita akajimensis DSM 45221]
 gi|293614043|gb|ADE54198.1| restriction modification system DNA specificity domain protein
           [Coraliomargarita akajimensis DSM 45221]
          Length = 447

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 130/459 (28%), Positives = 213/459 (46%), Gaps = 64/459 (13%)

Query: 3   HYKAYPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGKDII-----YIGLE-- 54
            YKAYP+Y+DSG  W+G +P  W V   K  F++ +    SESG + +     Y G++  
Sbjct: 4   RYKAYPEYRDSGFSWMGEVPSGWSVQRGKYVFSEFS--ERSESGNETLLSVSEYYGVKPR 61

Query: 55  -DVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV 113
            DV +  G++L     SR              ++   +  + R   +  +DGI S  + V
Sbjct: 62  GDVIA-DGEFL-----SRAESLVGYKFCKANDLVMNIMLAWKRGLGVTKYDGIVSPAYSV 115

Query: 114 LQPKDVLPELLQGWLLSIDV-TQRIEAICEGATMSHADW--KGIGNIPMPIPPLAEQVLI 170
            +  +        +LL  D+ T   +    G   S      +  G+  + +P L EQ  I
Sbjct: 116 FRFGEYADPDYMHYLLRTDLYTGHFKTRSTGVIDSRLRLYPESFGDTSILLPSLPEQKQI 175

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              +  ET +ID LI ++   I LLKEK+QA++S+ VTKGLNPD KMKDSG+EW+G VP+
Sbjct: 176 ARFLDHETAKIDRLIAKQQELIALLKEKRQAVISHAVTKGLNPDAKMKDSGVEWLGQVPE 235

Query: 231 HWEVKPFFALVTELNRKNTKLI-----ESNILSLSYGNIIQKLETRNMGLKPESYETYQI 285
           HWEV     +V    R    ++       N + +  G  ++    R   L   +Y     
Sbjct: 236 HWEVTYLTHIVDPSRRIMYGIVLPGPNVDNGVPIVKGGDVKPGRLRLDSLCKTTY----- 290

Query: 286 VDPGEIVFRFIDLQNDKRSLRSAQVME--RGIITSAYMAVKPHGIDSTYLA--------- 334
                     I+   ++  L++  ++   RG I    + + P  I+   L          
Sbjct: 291 ---------VIESNYERSRLKTGDIVYSIRGTIGD--VEIVPEEINGANLTQDAARIAPK 339

Query: 335 ------WLMRSYDLCKVFY-----AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
                 WLM +     VF      ++G+ +R  +   D+K+  +  PP  E+ DI   ++
Sbjct: 340 VPSDNRWLMYTMKSTSVFSQLEVGSLGAAVR-GINIRDLKKAIIPYPPQSERNDIEAFLD 398

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           ++  ++D L    ++ I LL+ERR++ I+AAVTG+ID+R
Sbjct: 399 IQLGKLDRLSVDCKRQIELLQERRTALISAAVTGKIDVR 437


>gi|146280647|ref|YP_001170800.1| type I restriction-modification system, S subunit [Pseudomonas
           stutzeri A1501]
 gi|145568852|gb|ABP77958.1| type I restriction-modification system, S subunit [Pseudomonas
           stutzeri A1501]
          Length = 421

 Score =  150 bits (380), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 127/443 (28%), Positives = 210/443 (47%), Gaps = 46/443 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M HYK YP YKDSGV+W+G +P+HW + P K   ++      E+G D      ++VE+  
Sbjct: 1   MSHYKPYPAYKDSGVEWLGRVPEHWTIGPYKATIQI------ENGSD-----YKEVEADD 49

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           G   P  G+      S+  ++    +L G+ G   +   +        T +  +    + 
Sbjct: 50  G--YPVIGSGGPFAYSSKLMYDGESVLLGRKGTIDKPLYVNGAFWAVDTMYWSI----IK 103

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
           P     +      T   +       +       +G+  +  P   EQ  I   +  ET R
Sbjct: 104 PGAHGRFAYYTATTIPFDMYSTNTALPSMTKSVLGSHVVAFPGFEEQQAIAGHLDRETAR 163

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID L+ ++IRFIELL+EK+QAL+++ VTKGL+P VKMKDSG+EW+G VP+HW +K F  +
Sbjct: 164 IDALVEKKIRFIELLREKRQALITHAVTKGLDPSVKMKDSGVEWLGAVPEHWVIKRFRDI 223

Query: 241 VTELNR-------KNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVF 293
              ++         N   I   I  ++  +II +  + +  +   +  T   +       
Sbjct: 224 CISISTGPFGTALGNEDYITGGIPVINPSHIIDEQCSPDPDI---TVSTETALRLSFWAM 280

Query: 294 RFIDLQNDKRS-LRSAQVM----ERGIITSAYMAVKPHGID--STYLAWLMRS------Y 340
           R  DL   +R  L  A ++    +  I  +  + V+P+     + YL  +++S       
Sbjct: 281 RAGDLVTARRGELGRAAIIFGEQDGWICGTGSLRVRPNPSQALTEYLHTVLQSRYAREWL 340

Query: 341 DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPP-IKEQFDITNVINVETARIDVLVEKIEQS 399
           +L  V   M + L + +    +  LP+ +PP   EQ  + + +  ++ R+  + +K   S
Sbjct: 341 NLASVGATMAN-LNEGI----LGSLPLALPPSTAEQEKLLSSLAAQSERLIKIEQKAALS 395

Query: 400 IVLLKERRSSFIAAAVTGQIDLR 422
           + LLKE RS+ I AAVTGQIDLR
Sbjct: 396 VALLKECRSALITAAVTGQIDLR 418


>gi|329115021|ref|ZP_08243776.1| Type-1 restriction enzyme StySJI specificity protein [Acetobacter
           pomorum DM001]
 gi|326695464|gb|EGE47150.1| Type-1 restriction enzyme StySJI specificity protein [Acetobacter
           pomorum DM001]
          Length = 434

 Score =  150 bits (379), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 130/462 (28%), Positives = 208/462 (45%), Gaps = 73/462 (15%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTK--------LNTGRTSESGKDIIYIGLED 55
           +  YP YK+SGV+WIG IP  W + P++            LN    S    DI Y G   
Sbjct: 3   FPKYPAYKNSGVEWIGEIPVGWIISPLRYLAHCLDGKRIPLNKEERSYKKGDIPYWGANC 62

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLG-PYLRKAIIADFDGICSTQFLVL 114
           +     ++L                F +  IL G+ G P+        FD      F + 
Sbjct: 63  IVDFVDEFL----------------FNQELILLGEDGAPF--------FDKTKEVSFYIN 98

Query: 115 QP-------------KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPI 161
           +P             ++  P+ L   L  ++ +  I    EG+T        +  I +PI
Sbjct: 99  EPIWPNNHVHVLKVFENFSPKFLVYSLNCVEYSSYI----EGSTRDKLTQNNMNRIVVPI 154

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           PPL EQ  I   +  E  +ID LI E+ R I LL EK+QA++S+ VTKGLNP+  MK+SG
Sbjct: 155 PPLPEQQAIASFLDRECGKIDALIAEQERLIALLAEKRQAVISHAVTKGLNPNAPMKESG 214

Query: 222 IEWVGLVPDHWEVKPFFALVTELNRKNTKLI------ESNILSLSY---GNIIQKLETRN 272
           I W+G+VP+ W+       V + N   T++       E + L +        I   + R 
Sbjct: 215 IPWIGMVPEGWDCSR-LRFVAQFNPSKTEISYIPLNEEVSFLPMEAIRDDGTINLEQKRK 273

Query: 273 MGLKPESYETYQIVDPGEIVFRFID--LQNDKRSLRSAQVMERGIITSAYMAVK--PHGI 328
           +      Y  ++ +D   IVF  I    +N K ++    +   G  T+  +  +  P  +
Sbjct: 274 ISDVQNGYTYFRDMD---IVFAKITPCFENGKGAVVKKLLRGIGFGTTELIVARSVPSRV 330

Query: 329 DSTYLAWLMRSYDLCK----VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINV 384
              YL    +S    K      Y  G   R S +F  V+   V +PP+ +Q  I + +++
Sbjct: 331 IPEYLFRFFQSDIFRKPAEASMYGAGGQKRVSERF--VRDFSVYLPPLPDQQAIASFLDL 388

Query: 385 ETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
             ++ID L+ + +  + L KERR++ I+AAVTG+ID+R +++
Sbjct: 389 TCSKIDTLIAEQKTMLTLCKERRAALISAAVTGKIDVRAQNK 430


>gi|238918474|ref|YP_002931988.1| restriction modification system DNA specificity domain protein
           [Edwardsiella ictaluri 93-146]
 gi|238868042|gb|ACR67753.1| restriction modification system DNA specificity domain protein
           [Edwardsiella ictaluri 93-146]
          Length = 441

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 119/445 (26%), Positives = 213/445 (47%), Gaps = 45/445 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M +YKAYP+YKDSGV+W+G +P+ W +  +K    +  G+  +S           V++  
Sbjct: 1   MANYKAYPEYKDSGVEWLGLVPESWTICRLKNLAAIKNGQDYKS-----------VQTDD 49

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           G   P  G+  Q   ++  ++ K  +L G+ G   +   I +      T +         
Sbjct: 50  G--YPVMGSGGQFTFASKFMYDKPSVLLGRKGTIDKPLYINEPFWTVDTMYYT------- 100

Query: 121 PELLQG----WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL-AEQVLIREKII 175
            EL +G    +L  + +T +         +     + + N    +P   +E+  I + + 
Sbjct: 101 -ELNEGFDARYLYYLALTIQFSRYSTNTALPSMTQEHLSNYKFSVPKAESERKKITKFLD 159

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            ET +ID LI ++ + IELLKEK+ A++S+ VTKGLNPDV MKDSG+EW+G VP+HW + 
Sbjct: 160 HETAKIDNLIEKQQQLIELLKEKRHAVISHAVTKGLNPDVPMKDSGVEWLGEVPEHWTIS 219

Query: 236 PF--FALVTELNR-----KNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP 288
                A   + +R      +  L++  ++ LS  N I   E         S E +  ++ 
Sbjct: 220 TLKHHAKFIDGDRGSEYPNDNDLVDDGVVFLSSKN-ISNWEINIDDANYISREKFNRLNR 278

Query: 289 GEIVFRFIDLQNDKRSLRSAQV----MERGIITSAYMAVK------PHGIDSTYLAWLMR 338
           G+ +   + ++    + R  ++     ER   ++A++  +       +  ++ +L  + +
Sbjct: 279 GKAINGDVIVKVRGSTGRIGELAIFETERLNKSTAFINAQMMIIRLKNSFNNRFLCNVAQ 338

Query: 339 SYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            +   +       G  +Q L       + ++VPPI EQ  I   + +E  R D L++   
Sbjct: 339 GHYWMEQLNVGAYGTAQQQLNNAIFSGMIMVVPPIDEQLTINKFLELEIKRFDGLIKNTS 398

Query: 398 QSIVLLKERRSSFIAAAVTGQIDLR 422
             I L++ERR++ I+AAVTG+ID+R
Sbjct: 399 NMIQLIQERRTALISAAVTGKIDVR 423


>gi|332975485|gb|EGK12375.1| type I restriction-modification system specificity determinant
           [Desmospora sp. 8437]
          Length = 461

 Score =  150 bits (378), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 134/457 (29%), Positives = 219/457 (47%), Gaps = 45/457 (9%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNT--GRTSESGKDIIYIGLEDVESGTG- 61
           + Y  YK+S + WIG +P HW V+P+KR  K N    +T   G  +      D +   G 
Sbjct: 14  RKYGSYKESNIAWIGKVPVHWDVLPMKRLDKNNMEMAQTGPFGSHLHASDYMDSDLKNGV 73

Query: 62  ---------------KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG- 105
                            +P+   S+  + S V    K  I++ ++G   R A +   +  
Sbjct: 74  PLILIKHVNDFKIIDHNMPRVSKSKAEELS-VYKLKKNDIVFSRVGTMGRVAPVTKKEEG 132

Query: 106 -ICSTQFLVL--QPKDVLPELLQGWLLSIDV-TQRIEAICEGATMSHADWKGIGNIPMPI 161
            + S Q L L  + KD+  + L  +LLS D+ T+ ++ +  G+T    +   + N+ +  
Sbjct: 133 WLISGQMLRLRIKSKDIDNQFLL-YLLSSDISTKYLQLVSVGSTRDSINTDILRNMVIVR 191

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           P L EQ  I   +  ET ++D L+ ++ R IELL+EK+QAL++  VTKGLNP+V MKDSG
Sbjct: 192 PSLPEQQAIANFLDRETGKLDRLVEKKQRLIELLREKRQALITQAVTKGLNPNVPMKDSG 251

Query: 222 IEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI----IQKLETRNMGLKP 277
           IEW+G VP+HW+V     L       + + IE  I   + G      I  + + NM LK 
Sbjct: 252 IEWLGEVPEHWKVLKIKWLSKVKRGASPRPIEDPIYFDNNGEYAWVRIADVTSSNMYLKK 311

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLM 337
            S    ++   G  +   + L   K  L  A  + +  I+     +    +   Y   L 
Sbjct: 312 TSQTLSEL---GASL--SVKLPPGKLFLSIAGSVGKPCISGIKCCIHDGFV---YFPDLQ 363

Query: 338 RSYDLCKVFYAMGS--------GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
            +       +A G+        G + +L  + V  +   VP IKEQ +I   ++ +T++I
Sbjct: 364 ENEKFFYYVFASGAPYGGLGKLGTQLNLNTDIVGDIYTGVPEIKEQLEIVKYLDNQTSKI 423

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
           D L+ K++  I  +KE R + I+AAVTG+ID++ + Q
Sbjct: 424 DTLISKLQTQITKIKEYRQALISAAVTGKIDVQEKVQ 460


>gi|327479499|gb|AEA82809.1| restriction modification system DNA specificity domain protein
           [Pseudomonas stutzeri DSM 4166]
          Length = 491

 Score =  149 bits (377), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 131/455 (28%), Positives = 211/455 (46%), Gaps = 42/455 (9%)

Query: 3   HYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNT----GRTSESGKDIIYIGLEDVES 58
           ++  YP YKDSGV+W+G +P+HW +  +KR     T    G   +   D+  I + D + 
Sbjct: 27  NFPTYPAYKDSGVEWLGEVPEHWAIFSLKRSVDGCTNGLWGDEPDGENDLAVIRVADFDR 86

Query: 59  GTGKYLPKDGNSRQSDTS---TVSIFAKGQILYGKLGPYLRKAIIA------DFDGICST 109
            T + +  D  + +S T       +   G +L  K G   +  +        DF+ I S 
Sbjct: 87  ATCR-VGLDKLTYRSITQKERASRLLQSGDLLIEKSGGGEKTLVGCVVLFEHDFEAITSN 145

Query: 110 QFLVLQPKDVLPELLQGWLL-SIDVTQR----IEAICEGATMSHADWKGIGNIPMPIPPL 164
               ++P   L     G+L  S D   +      AI +   + + D +         P L
Sbjct: 146 FVARMRP---LHGFDSGFLCYSFDSLYQGKVNFPAIKQTTGIQNLDSESYLQERFCFPTL 202

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
           AEQ  I   +  ET RID LI E+ R IELLKEK+QA++S+ VTKGL+P V MKDSG+EW
Sbjct: 203 AEQTQIARFLDHETARIDALIEEQQRLIELLKEKRQAVISHAVTKGLDPTVPMKDSGVEW 262

Query: 225 VGLVPDHWEVKP--FFALVTELNRKNTKLIESNILSLSY-------GNIIQKLETRNMGL 275
           +G VP HW V    ++A +     K         + + Y          +   E + + +
Sbjct: 263 LGEVPAHWNVGTLRWYATIQGGVAKGKDYEGRETVVMPYLRVANVQNGYVDLAEVKEIAV 322

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY----MAVKPHG-IDS 330
                E Y++   G+++   ++   D   L    V +  I    +     A++P+G + +
Sbjct: 323 LESEVERYRL-RAGDVL---MNEGGDNDKLGRGTVWQAQIDPCLHQNHVFAIRPNGLLRA 378

Query: 331 TYLAWLMRSYDLCKVFY--AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
            +LA   ++      FY  +  S    S+   +V  L + +P  KEQ +I   +  +  R
Sbjct: 379 EWLAAFTQAEQARTYFYLNSKQSTNLASISASNVMSLALPIPSEKEQLEILTYLEADRIR 438

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            + L      ++ LL+ERRS+ I+AAVTG+ID+RG
Sbjct: 439 HEELTAVAVSTVELLQERRSALISAAVTGKIDVRG 473


>gi|73668548|ref|YP_304563.1| hypothetical protein Mbar_A1015 [Methanosarcina barkeri str.
           Fusaro]
 gi|72395710|gb|AAZ69983.1| hypothetical protein Mbar_A1015 [Methanosarcina barkeri str.
           Fusaro]
          Length = 477

 Score =  149 bits (376), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 137/459 (29%), Positives = 219/459 (47%), Gaps = 45/459 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVES-G 59
           ++ +K YP+YKDSGV+WIG IPK W+V  IK  T +  GR       I + GL+  E   
Sbjct: 27  IREWKRYPEYKDSGVEWIGEIPKEWEVKKIKHTTYVK-GR-------IGWQGLKSDEFID 78

Query: 60  TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLR---KAIIADFDGICSTQFLVLQP 116
            G +L    +      +  S +   +  Y +  PY++   K ++   DG      LV + 
Sbjct: 79  EGPFLVTGTDFINGSVNWGSCYHVNEERYNE-DPYIQLKEKDLLITKDGTIGKVALVTRL 137

Query: 117 KD--------VLPELLQG--------WLLSIDVTQRI-EAICEGATMSHADWKGIGNIPM 159
           K          L   L G        WLL+ +V +     I  G+T+ H           
Sbjct: 138 KTKATLNSGIFLTRPLTGEYYTNFMYWLLNSEVFETFFNYISNGSTIQHLYQNVFVIFSF 197

Query: 160 PIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKD 219
           P+P L+EQ  I   +  ET +I+TLI ++ R IELL+EK+ AL+S+ VTKGL+P  K K+
Sbjct: 198 PLPSLSEQQSIVSFLDRETSKIETLIEKKQRLIELLEEKRSALISHAVTKGLDPYAKKKN 257

Query: 220 SGIEWVGLVPDHWEVKPFFALVTELNRKNTK------LIESNILSLSYGNI-IQKLETRN 272
           SG+EWVG +P+ W +     L +++    T         +S IL L   N+    L   +
Sbjct: 258 SGVEWVGEIPEGWFLSKLKYLTSKIGSGKTPRGGSEIYCDSGILFLRSQNVHFDGLRLDD 317

Query: 273 MGLKPESYETYQI---VDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP--HG 327
           +    ES ++      V P +++   I   +  RS    +   +  +      ++P    
Sbjct: 318 VVYIDESIDSEMSSTRVLPDDVLLN-ITGASIGRSSIVPKDFPQANVNQHVCIIRPLKKK 376

Query: 328 IDSTYLAWLMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVP-PIKEQFDITNVINVE 385
           IDS  L + + S  +  + ++  +G  R+ L F  +    + +P  + EQ  I N ++ +
Sbjct: 377 IDSRLLHYELSSNGVQALIFSNENGTSREGLTFSQISNFVIAIPNNLDEQRHIANFLDHK 436

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           T +ID  + KI   I  LKE R++ I+AAVTG+ID+R E
Sbjct: 437 TEKIDTFINKISAQIEKLKEYRTALISAAVTGKIDVREE 475


>gi|71064986|ref|YP_263713.1| type I restriction-modification system S subunit [Psychrobacter
           arcticus 273-4]
 gi|71037971|gb|AAZ18279.1| possible type I restriction-modification system, S subunit
           [Psychrobacter arcticus 273-4]
          Length = 457

 Score =  149 bits (375), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 121/453 (26%), Positives = 215/453 (47%), Gaps = 41/453 (9%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT--G 61
           Y+ Y +YKDSGV+W+G IP HW++  ++       G T  +  D++  G+  V  G    
Sbjct: 8   YQRYAEYKDSGVEWLGKIPSHWELSKLRYMFSFGRGLTI-TKADLLDTGVPCVNYGEVHS 66

Query: 62  KYL----PKDGNSRQSD-----TSTVSIFAKGQILYGKLGPYLRKA-----IIADFDGIC 107
           KY     PK    +  D     +S  ++  +G +++      +  +     +++D     
Sbjct: 67  KYGFEVDPKRHYLKCVDEGYLQSSPYALLTQGDLVFADTSEDIEGSGNFTQLVSDDLIFA 126

Query: 108 STQFLVLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
               ++ +P D        +L+ S ++  ++  + +G  +       +  + + +P L E
Sbjct: 127 GYHTVIARPFDRQCSRFYAYLMDSKEIRTQVRHMVKGVKVFSITQSILKGVRIWLPSLDE 186

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           +  I   +  ET +IDTLI ++   I+LLKEK+QA++S+ VTKGLNPD  +KDSG+EW+G
Sbjct: 187 RETIANFLDFETAQIDTLIDKQKTLIQLLKEKRQAVISHAVTKGLNPDAPLKDSGVEWLG 246

Query: 227 LVPDHWEVKPFFALVTELNR--KNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQ 284
            VP+HW V     L++E  +   N    + +     +  I   L   N  LK +++ +  
Sbjct: 247 EVPEHWGVSKLKYLISEPLQYGANEAAEDVDKTQPRFVRITDVLPNGN--LKDDTFRSL- 303

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIIT---------SAYMAVKPHGIDSTYLAW 335
              P EI   ++ +  D    RS   + +  I          + Y+       + T   W
Sbjct: 304 ---PQEIAEPYMLMDGDVLLARSGGTVGKSFIYRDSWGKCCFAGYLIKAKIDEEITPAEW 360

Query: 336 LMRSYDLCKVFYAMGSGLR-----QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
              +  L   ++     ++     Q++  +      + VPP++E + I + IN      D
Sbjct: 361 FYLN-TLTDFYWKWIESIQIQATIQNVSADKYNSFVIAVPPLEESYKIISYINYNLEVFD 419

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            LV K EQ+I L++ERR++ I+AAVTG+ID+RG
Sbjct: 420 TLVMKAEQAIQLMQERRTALISAAVTGKIDVRG 452


>gi|56421440|ref|YP_148758.1| type I restriction-modification system specificity determinant
           [Geobacillus kaustophilus HTA426]
 gi|56381282|dbj|BAD77190.1| type I restriction-modification system specificity determinant
           [Geobacillus kaustophilus HTA426]
          Length = 438

 Score =  148 bits (374), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 123/439 (28%), Positives = 210/439 (47%), Gaps = 23/439 (5%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY---------I 51
           M + K YP+YKDSGV+W+  +P  W+V+ IKR T++  G +     D IY         +
Sbjct: 1   MVNLKKYPKYKDSGVEWLREVPSEWQVLQIKRLTRVRRGASPRPIDDPIYFDDNGEYSWV 60

Query: 52  GLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQF 111
            + DV + +  YL +      +  S++S+  +   L+  +   + K  I +    C    
Sbjct: 61  RISDV-TKSNMYLEETEQKLSNLGSSLSVKLEPGELFLSIAATVGKPCITNVK-CCIYDG 118

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
            V  P     +    ++       R   + +  T  + +   +G+I + +P + EQ +I 
Sbjct: 119 FVYFPDYRGDKRFLYYIFEAGEAYR--GLGKLGTQLNLNTDTVGSIYIAVPTIQEQKMIS 176

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
           + +  +   ID+LI ++ + IELL+EK+Q +++  VTKGLNP+VKMKDSG+EW+G +P+ 
Sbjct: 177 DFLDEKVHEIDSLIADKEKLIELLEEKRQVIITEAVTKGLNPNVKMKDSGVEWIGEMPES 236

Query: 232 WEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEI 291
           WEV        ++N+          L + Y + I  + +R   +  E Y           
Sbjct: 237 WEVSK-IKYQADINKYTLSENTDEDLEIKYID-ISSVNSRGEVVNIEKYYFKDAPSRARR 294

Query: 292 VFRFID--LQNDKRSLRS----AQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCK 344
           + R  D  +   +  L++     +V E  I ++ +  + P   I   YL +LMRS     
Sbjct: 295 ILRKGDTIISTVRTYLKAITWFEEVEENLICSTGFAVLSPKETIYPKYLFYLMRSTKYID 354

Query: 345 VFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
                  G+   ++   ++  +  L+P I EQ  I   I+ E  +ID LV++I+  I  L
Sbjct: 355 EIVKRSIGVSYPAITSTEIGMMECLLPNINEQKMIVEYIDNELKKIDGLVDEIKLQIQKL 414

Query: 404 KERRSSFIAAAVTGQIDLR 422
           KE R S I  AVTG+ID+R
Sbjct: 415 KEYRQSLIYEAVTGKIDVR 433


>gi|169634728|ref|YP_001708464.1| putative type I restriction-modification system specificity
           determinant for hsdM and hsdR (HsdS) [Acinetobacter
           baumannii SDF]
 gi|169153520|emb|CAP02682.1| putative type I restriction-modification system specificity
           determinant for hsdM and hsdR (HsdS) [Acinetobacter
           baumannii]
          Length = 433

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 119/447 (26%), Positives = 207/447 (46%), Gaps = 47/447 (10%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           +K YP YK+SGV+W+G +P+HW++V  K     N  +      D I     D +    K 
Sbjct: 3   FKQYPSYKNSGVEWLGDVPEHWQIVRTKDI--FNHRKEEALEDDEIVTAFRDGQVTLRKN 60

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLP 121
              DG +             G ++  ++  +     ++D  G  +  + V   K+  +  
Sbjct: 61  RRTDGFTNSIKEHGYQHINSGDLVIHEMDAFAGAIGVSDSSGKSTPVYTVCYAKNENINH 120

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHAD--WKGIGNIPMPIPPLAEQVLIREKIIAETV 179
                +  ++  T  I ++ +G  +   +  W    N+ +  PP A+Q  I   +  ET 
Sbjct: 121 HFYSHFFRTMAKTGFINSLAKGIRVRSTEFRWNESRNVYLVEPPKADQEKIVSFLDTETA 180

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
           RID LI+++ + IELL+E++++++S+ VTKGLNP+  MKDSG+EW+G VP+HW+      
Sbjct: 181 RIDNLISKQEKLIELLEEQRKSIISHAVTKGLNPNAPMKDSGVEWLGDVPEHWD------ 234

Query: 240 LVTELNRKNTKLIESNILSLSY--GNIIQKLETRNMGLKPESYETYQIVDPGEIVFR--- 294
            +T L     K I  +I+ L+Y    I    +   + L+  + +  Q+     +  +   
Sbjct: 235 -ITRL-----KNIGKSIIGLTYSPNEICDADDDSYLVLRSSNVQNGQLSFLDNVYVKSSV 288

Query: 295 -----------FIDLQNDKRSLRSAQVM----ERGIITSAYMAVKPHGIDSTYLAWLMRS 339
                       I  +N  R L    ++     +     A+M V      + Y+ W++ S
Sbjct: 289 SEKLKIKKNDILICSRNGSRDLIGKNIIIKNPPKNSTFGAFMTVYRSEY-ADYVYWILNS 347

Query: 340 YDLCKVFYAM-GSGLRQS---LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           Y    +F A  GS L  +   L   ++  + V   PI EQ +I   ++ E  + + L+ K
Sbjct: 348 Y----IFKAQAGSYLTTTVNQLTINNLNNMTVPFAPISEQDEIVEFLSTENLKFNNLISK 403

Query: 396 IEQSIVLLKERRSSFIAAAVTGQIDLR 422
            +  I  LKE R+S I+ AVTG+ID+R
Sbjct: 404 QKALIEKLKEYRASIISHAVTGKIDVR 430


>gi|308171852|ref|YP_003915182.1| type I restriction-modification system specificity subunit
           [Arthrobacter arilaitensis Re117]
 gi|307743224|emb|CBQ74047.1| type I restriction-modification system specificity subunit
           [Arthrobacter arilaitensis Re117]
          Length = 449

 Score =  147 bits (372), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 128/451 (28%), Positives = 209/451 (46%), Gaps = 54/451 (11%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY- 63
           K YP+YKDSGV+W+G IP  W   P+    K    RT   G      G E++ S    Y 
Sbjct: 4   KPYPKYKDSGVEWLGEIPIDWSTFPLWNLFK----RTKRLGN-----GKEELLSVYRDYG 54

Query: 64  -LPKDG-----NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
            +PK       N    D S   I   G ++  K+  +     +++ +GI S  + V +  
Sbjct: 55  VVPKSSRNDNFNKASEDLSKYQIVEIGDLVINKMKAWQGSVAVSEHNGIVSPAYFVFRAL 114

Query: 118 DVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPI--PPLAEQVLIREKI 174
                    +L+ S    Q   +I  G   +  D   + +  MP+  P L+EQ  I   +
Sbjct: 115 GKADSRFIHFLMRSTPYFQHYASISAGVRPNQWDLDPVRHRKMPVLFPSLSEQRYIAAYL 174

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             ET  ID  I ++   I LL E++ A ++  VTKGL+P  +MKDS +  +GL+P  W  
Sbjct: 175 DRETAEIDAFIADQEELIALLSERRTATITQAVTKGLDPKSRMKDSNVSNLGLIPAPWA- 233

Query: 235 KPFFALVTELNRKNTKLIE-SNILSLSYGNIIQKLETRNMG-----------LKPESYE- 281
                 VT L     K+ + ++I   + G I   + TR++              PE+YE 
Sbjct: 234 ------VTGLKHFTLKITDGAHISPETDGGIYDFVSTRDVSDSGINFEGSLKTSPETYEY 287

Query: 282 ---TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERG--IITSAYMAVKP--HGIDSTYLA 334
              T      G+++F       D    R+  V      ++ S+ + ++P    +D  +L 
Sbjct: 288 MVRTGCRPQNGDVLF-----SKDGTVGRTVVVQGNHDFVVASSLIIIRPDLSKLDPNFLN 342

Query: 335 WLMRSYDLCKVF--YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           +L RS  + +    +  G+GL + L   ++ R+  + PP+ EQ +I + ++ ET  ID  
Sbjct: 343 YLCRSAFVQEQVRSFVKGAGLPR-LSIANLLRVTGVFPPLNEQQEIVDYLDRETTEIDAA 401

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           +    ++I L KERR++ I+AAVTG+ID+RG
Sbjct: 402 IADAREAIALSKERRAAVISAAVTGKIDVRG 432


>gi|119491619|ref|ZP_01623491.1| hypothetical protein L8106_03529 [Lyngbya sp. PCC 8106]
 gi|119453348|gb|EAW34512.1| hypothetical protein L8106_03529 [Lyngbya sp. PCC 8106]
          Length = 433

 Score =  147 bits (370), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 136/451 (30%), Positives = 211/451 (46%), Gaps = 51/451 (11%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY--IGLEDVES 58
           MK YK+Y   K SGV+W+G IP+HW++  +K    L  G++ +S  D  Y  IG+  ++ 
Sbjct: 1   MKKYKSYSTDKPSGVEWLGNIPEHWELRKLKFIADLIMGQSPDS-TDYNYEEIGVPFLQ- 58

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK- 117
           GT ++   + N R S  S      K  +L     P     +     GI       ++PK 
Sbjct: 59  GTAEFGIINPNPRLSCESAKKYARKDDLLLSVRAPVGEINVADQVYGI-GRGLCAIRPKI 117

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADW---KGIGNIPMPIPPLAEQVLIREKI 174
           +V  +    + L I    ++E +  GAT S  D      + N+    PPL EQ LI   +
Sbjct: 118 NVFNKTFTRYFLEIG---KVELV-SGATGSIYDAVTVNQVANLQCLTPPLKEQKLIATFL 173

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             ET RIDTLIT++   I LL++K+ A+++  VTKGL P++ MKDSG+EW+G VP +WEV
Sbjct: 174 DRETTRIDTLITKKCELINLLEKKRTAIITNAVTKGLEPELPMKDSGVEWLGKVPRNWEV 233

Query: 235 KPFFALV-------TELNRKNTKLIESNILSLSYGNII---QKLETRNMGLKPESYETYQ 284
           K    +        T   R + +  + N   +  G+I    + + +    L        +
Sbjct: 234 KKLKYIAQIVRGKFTHRPRNDPRFYDGNYPFIQTGDISAANKYITSYQQTLNELGLSVSK 293

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK 344
               G +V              +A + +  I+   + A  P  I    + +L R+Y L  
Sbjct: 294 EFPKGTLVMTI-----------AANIGDLAILD--FPACFPDSI----VGFLPRNYCLDF 336

Query: 345 VFY---AMGSGL--------RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
           ++Y   AM S +        + +L  E +  L  + PPI  Q  I   ++    RID L+
Sbjct: 337 LYYNLTAMKSEMVKTATLNTQMNLNIERIGGLFSICPPIAIQKQIATYLDKVNIRIDELI 396

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           +K   SI  L + R S I AAVTG+ID+R E
Sbjct: 397 DKTATSISELTKYRQSLITAAVTGKIDVREE 427


>gi|145633684|ref|ZP_01789410.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 3655]
 gi|144985444|gb|EDJ92265.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 3655]
          Length = 418

 Score =  147 bits (370), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 118/429 (27%), Positives = 204/429 (47%), Gaps = 30/429 (6%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + Y  YKDSGV+W+G +P HW+   +KR  +L   +  +       + L       GK +
Sbjct: 2   RRYESYKDSGVEWLGEVPSHWE---LKRLKQLFVEKKHKQN-----LSLNCGAISFGKVI 53

Query: 65  PK-DGNSRQSDTSTVSIFAKGQILYGKLGP-----YLRKAIIADFDGICSTQFLVLQPKD 118
            K D    ++   +     KG+ L   L        LR A+ ++ D + S  ++VL+ K 
Sbjct: 54  EKADDKVTEATKRSYQEVLKGEFLINPLNLNYDLISLRIAL-SEIDVVVSAGYIVLKEKQ 112

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           ++ +    +LL       ++ +  G   +  ++  I +  + IPPL+EQ  I + +  +T
Sbjct: 113 IINKKYFSYLLHRYDVAYMKLLGSGVRQT-INYGHISDSILVIPPLSEQQKIAQFLDDKT 171

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HW+V+   
Sbjct: 172 AKIDRAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWDVQRSK 231

Query: 239 ALVTELNRKNTKLIESNILS-LSYGNIIQKLETRNMGLKPESYET-YQIVDPGEIVFRFI 296
            +  ++ RK  +  E  I++    G +  +   R  G      E  YQ +  G++V   +
Sbjct: 232 FIFKKIERKVNE--EDQIVTCFRDGQVTLRANRRTEGFTNALKEHGYQGIRKGDLVIHAM 289

Query: 297 DLQNDKRSLRSAQVMERGIITSAYMAVKPHG---IDSTYLAWLMRSYDLCKVFYAMGSGL 353
           D       +  +     G  T  Y    PH    ID  + A+ +R+  L     ++  G+
Sbjct: 290 DAFAGAIGISDSD----GKATPVYSVCLPHNKQKIDVYFYAYYLRNLALSGFISSLAKGI 345

Query: 354 RQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
           R+     ++ D   L + +PP  EQ  I + ++ +T++ID ++      I  LKE +S  
Sbjct: 346 RERSTDFRYADFAELLLPIPPYLEQQKIADYLDKQTSKIDQVIALKTAHIEKLKEYKSVL 405

Query: 411 IAAAVTGQI 419
           I   VTG++
Sbjct: 406 INDVVTGKV 414


>gi|254491851|ref|ZP_05105030.1| Type I restriction modification DNA specificity domain protein
           [Methylophaga thiooxidans DMS010]
 gi|224463329|gb|EEF79599.1| Type I restriction modification DNA specificity domain protein
           [Methylophaga thiooxydans DMS010]
          Length = 454

 Score =  146 bits (369), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 124/458 (27%), Positives = 204/458 (44%), Gaps = 59/458 (12%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           Y  Y QY+   + W    PK W +  +K  + +N G++  S              G  ++
Sbjct: 8   YAPYSQYETVALPWFDTKPKEWMLTRLKFTSSINMGQSPNSDDCNDEGHGRPFLQGNAEF 67

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPEL 123
             +   ++    +     ++G +L     P     I     GI       +  + V  + 
Sbjct: 68  GMRTPKAKLFCEAAKKTCSEGDVLLSVRAPVGELNIANQEYGI-GRGLCAITAQSVKADF 126

Query: 124 LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDT 183
           +  WLL   V+Q + A+  G+T      + + N+   +P  +EQ  I   +  ET +ID 
Sbjct: 127 MW-WLLQASVSQ-LRAVATGSTFQAVSAEQVSNLTCLLPAQSEQTQIATFLDRETAKIDR 184

Query: 184 LITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF-----F 238
           LI ++ R I+LL+EK+QA++S+ VTKGLNPDV MKDSG+EW+G +P  W +        F
Sbjct: 185 LIEKQQRLIKLLEEKRQAVISHAVTKGLNPDVPMKDSGVEWLGEIPSMWSIVQLRRGIDF 244

Query: 239 ALVTELN------RKNTKLIESNILSLSYGNIIQKLETRNMGL---------KPESYETY 283
               E N      +KN  L   N    ++      LE R  GL         K  SY + 
Sbjct: 245 LTDFEANGSFAEVKKNVSLDTDN--KYAWYVRATDLEHRRFGLVDGNRSCNEKSYSYLSK 302

Query: 284 QIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM--------AVKPH----GIDST 331
             +D GE++                 V +RG I   Y+         + P+     ++  
Sbjct: 303 TTLDGGELL-----------------VAKRGEIGKVYLMPEIDCRATLAPNLYLIRLNDN 345

Query: 332 YLA-----WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVET 386
           +       W + SY   ++  A  S    +L  +DV+   + +PP++EQ  I   I+  T
Sbjct: 346 FFPQFTYYWFISSYGKSELVNADKSTTIGALYKDDVRACIIPMPPVQEQILIVKHISERT 405

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
            +I  L+ K+++SI L  ERR++ I+AAVTG+ID+R +
Sbjct: 406 DKIQRLITKVQKSIALSTERRAALISAAVTGKIDVRDQ 443


>gi|189499714|ref|YP_001959184.1| putative type I restriction-modification system [Chlorobium
           phaeobacteroides BS1]
 gi|189495155|gb|ACE03703.1| putative type I restriction-modification system [Chlorobium
           phaeobacteroides BS1]
          Length = 436

 Score =  146 bits (368), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 126/459 (27%), Positives = 219/459 (47%), Gaps = 70/459 (15%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           +  YP+YK SGV+W+G +P+HW+++  +R    +  + S    DI         S T KY
Sbjct: 3   FPRYPKYKASGVEWLGEVPEHWQMINSRRL--FHQAKESPLTDDIQL-------SATQKY 53

Query: 64  --LPKDGNSRQSDTSTVSIFAKGQILYGKLGPY------LRKAI-IADFDGICSTQFLVL 114
             +P+           +++   G   + ++  +       +  I  + + G  S  + VL
Sbjct: 54  GVVPQSLFMESDGKVALALSGLGNFKHVEVDDFVISLRSFQGGIERSKYSGCVSPAYTVL 113

Query: 115 QPKDVLPELLQGWLLS----IDVTQRI-EAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
           +P + +     G+LL     +++ Q + + + +G ++S+  +   G IP+P PPLAEQ  
Sbjct: 114 RPAEPIDGSYWGFLLKSRRYVEILQTMNDGLRDGKSISYQQF---GQIPLPSPPLAEQTA 170

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV- 228
           I E +  ET +ID L+ E+ R +ELLKEK+QA++S+ VTKGLNP   MK SGIEW+G V 
Sbjct: 171 IAEFLDRETGKIDELVAEQRRLMELLKEKRQAVISHAVTKGLNPHAPMKPSGIEWLGDVP 230

Query: 229 --------------------PDHWEVK-----PFFALVTELNRKNTKLIESNILSLSYGN 263
                               PD ++ +     PFF +   +N  + +++     +++   
Sbjct: 231 VGWSVLKLGNISRFKGGAGFPDSYQGQTDNEIPFFKVGDMVNADDARVMRRANHTITEAT 290

Query: 264 IIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV 323
                E R   + PES   +  V    ++ R+  L             +R  I +  M +
Sbjct: 291 ---ARELRAF-VFPESTIVFAKVGAALLLKRYRLLG------------QRSCIDNNMMGM 334

Query: 324 KPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
                D + + +L+    L  +   +  G   S+    +    + +PPI EQ +I   + 
Sbjct: 335 TVG--DGSSVDYLLYVLPLLDLELIVNPGAVPSINEGQISGQRIALPPIDEQREIVEFLT 392

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
             TA+ D L  + +++I LL+ERR++ I+AAVTGQID+R
Sbjct: 393 SVTAKFDTLTAEAQRTIDLLQERRTALISAAVTGQIDVR 431


>gi|68248718|ref|YP_247830.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 86-028NP]
 gi|319896548|ref|YP_004134741.1| type i site-specific restriction-modification system, s subunit
           [Haemophilus influenzae F3031]
 gi|68056917|gb|AAX87170.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 86-028NP]
 gi|317432050|emb|CBY80399.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae F3031]
          Length = 416

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 118/429 (27%), Positives = 203/429 (47%), Gaps = 30/429 (6%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + Y +YKDSGV W+G +P HW+   +KR  +L   +  +       + L       GK +
Sbjct: 2   RRYERYKDSGVDWLGEVPSHWE---LKRLKQLFVEKKHKQS-----LSLNCGAISFGKVI 53

Query: 65  PK-DGNSRQSDTSTVSIFAKGQILYGKLGP-----YLRKAIIADFDGICSTQFLVLQPKD 118
            K D    ++   +     KG+ L   L        LR A+ ++ D + S  ++VL+ K 
Sbjct: 54  EKSDDKVTEATKRSYQEVLKGEFLINPLNLNYDLISLRIAL-SEIDVVVSAGYIVLKEKQ 112

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           ++ +    +LL       ++ +  G   +  ++  I +  + IPPL+EQ  I + +  +T
Sbjct: 113 IINKKYFSYLLHRYDVAYMKLLGSGVRQT-INYGHISDSILVIPPLSEQQKIAQFLDDKT 171

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HW+V+   
Sbjct: 172 AKIDQAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWDVQRSK 231

Query: 239 ALVTELNRKNTKLIESNILS-LSYGNIIQKLETRNMGLKPESYET-YQIVDPGEIVFRFI 296
            +  ++ RK  +  E  I++    G +  +   R  G      E  YQ +  G++V   +
Sbjct: 232 FIFKKIERKVNE--EDQIVTCFRDGQVTLRANRRTEGFTNALKEHGYQGIRKGDLVIHAM 289

Query: 297 DLQNDKRSLRSAQVMERGIITSAYMAVKPHG---IDSTYLAWLMRSYDLCKVFYAMGSGL 353
           D       +  +     G  T  Y    PH    ID  + A+ +R+  L     ++  G+
Sbjct: 290 DAFAGAIGISDSD----GKATPVYSVCLPHDKQKIDVYFYAYYLRNLALSGFISSLAKGI 345

Query: 354 RQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
           R+     ++ D   L + +PP  EQ  I + ++ +T++ID  +      I  LKE +S  
Sbjct: 346 RERSTDFRYSDFAELLLPIPPYLEQQKIADYLDKQTSKIDRAIALKTAHIEKLKEYKSVL 405

Query: 411 IAAAVTGQI 419
           I   VTG++
Sbjct: 406 INDVVTGKV 414


>gi|148263547|ref|YP_001230253.1| restriction endonuclease S subunits-like protein [Geobacter
           uraniireducens Rf4]
 gi|146397047|gb|ABQ25680.1| Restriction endonuclease S subunits-like protein [Geobacter
           uraniireducens Rf4]
          Length = 443

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 129/456 (28%), Positives = 223/456 (48%), Gaps = 60/456 (13%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLE--------- 54
           Y+AYP+YKDSG +W+G +P HW+V+ IK  + +  G +     D  Y   E         
Sbjct: 5   YQAYPEYKDSGEEWLGDVPSHWEVIQIKHLSTVRRGASPRPIDDAKYFDDEGEYAWTRIA 64

Query: 55  DVESGTGKYLPKDGNSRQSD-TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV 113
           DV + +  YL  +   R SD  S++S+  +   L+  +   + K  I      C     V
Sbjct: 65  DV-TASEMYL-FNAPQRLSDLGSSLSVKLEPGALFLSIAGTVGKPCITGMKA-CIHDGFV 121

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
             P+  +P     ++ + +  Q  + + +  T  + +   +G I +     ++   I + 
Sbjct: 122 YFPELKIPSKFLFYVFAGE--QAYKGLGKFGTQLNLNTDTVGGIKIGCTENSQLEKIVQF 179

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  ET +IDTLI ++ + I+LLKEK+QA++S+ VTKGLNPD  MKDSG+EW+G VP+HW+
Sbjct: 180 LDHETAKIDTLIDKQQQLIKLLKEKRQAVISHAVTKGLNPDAPMKDSGVEWLGEVPEHWD 239

Query: 234 V---KPFFALVTE-----LNRKNTKLIESNILSLSYG--NIIQKLETR--------NMGL 275
           V   K     +T+      + KN +    +I  +  G  N    L T         N G 
Sbjct: 240 VCLAKFKTHAITDGAHISPDTKNGEHYFVSIKDMCDGLINFEDALLTSKESYKYLVNTGC 299

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER--GIITSAYMAVKPH--GIDST 331
           KPE         PG+I+F       D    ++    E    ++ S+ + +KP+   +   
Sbjct: 300 KPE---------PGDILF-----SKDGTIGKTVVTPENVDFVVASSLIIIKPNLKKLSPQ 345

Query: 332 YLAWLMRSYDLCKV-----FYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVET 386
           +  +L +S   C +      +  G+ L++ L  +++ ++  + PP+ EQ  I   I+ + 
Sbjct: 346 FFDYLCQS---CVIQEQVNSFVKGAALKR-LSIQNLLKVWGVFPPLDEQVVIAKHIDKKL 401

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            R   + +    +I L++ERR++ I+AAVTG+ID+R
Sbjct: 402 IRYQQIEQTANNAIALMQERRTALISAAVTGKIDVR 437


>gi|260581977|ref|ZP_05849772.1| restriction endonuclease S [Haemophilus influenzae NT127]
 gi|260094867|gb|EEW78760.1| restriction endonuclease S [Haemophilus influenzae NT127]
          Length = 416

 Score =  145 bits (365), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 117/429 (27%), Positives = 204/429 (47%), Gaps = 30/429 (6%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + Y +YKDSGV+W+G +P HW+   +KR  +L   +  +       + L       GK +
Sbjct: 2   RRYERYKDSGVEWLGEVPSHWE---LKRLKQLFVEKKHKQS-----LSLNCGAISFGKVI 53

Query: 65  PK-DGNSRQSDTSTVSIFAKGQILYGKLGP-----YLRKAIIADFDGICSTQFLVLQPKD 118
            K D    ++   +     KG+ L   L        LR A+ ++ D + S  ++VL+ K 
Sbjct: 54  EKSDDKVTEATKRSYQEVLKGEFLINPLNLNYDLISLRIAL-SEIDVVVSAGYIVLKEKQ 112

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           ++ +    +LL       ++ +  G   +  ++  I +  + IPPL+EQ  I + +  +T
Sbjct: 113 IINKKYFSYLLHRYDVAYMKLLGSGVRQT-INYGHISDSILVIPPLSEQQKIAQFLDDKT 171

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HW+V+   
Sbjct: 172 AKIDQAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWDVQRSK 231

Query: 239 ALVTELNRKNTKLIESNILS-LSYGNIIQKLETRNMGLKPESYET-YQIVDPGEIVFRFI 296
            +  ++ RK  +  E  I++    G +  +   R  G      E  YQ +  G++V   +
Sbjct: 232 FIFKKIERKVNE--EDQIVTCFRDGQVTLRANRRTEGFTNALKEHGYQGIRKGDLVIHAM 289

Query: 297 DLQNDKRSLRSAQVMERGIITSAYMAVKPHG---IDSTYLAWLMRSYDLCKVFYAMGSGL 353
           D       +  +     G  T  Y    PH    ID  + A+ +R+  L     ++  G+
Sbjct: 290 DAFAGAIGISDSD----GKATPVYSVCLPHDKQKIDVYFYAYYLRNLALSGFISSLAKGI 345

Query: 354 RQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
           R+     ++ D   L + +PP  EQ  I + ++ +T++ID  +      I  LKE ++  
Sbjct: 346 RERSTDFRYSDFAELLLPIPPYLEQQKIADYLDKQTSKIDRAIALKTAHIEKLKEYKNVL 405

Query: 411 IAAAVTGQI 419
           I   VTG++
Sbjct: 406 INDVVTGKV 414


>gi|53718590|ref|YP_107576.1| putative type I restriction enzyme specificity protein
           [Burkholderia pseudomallei K96243]
 gi|52209004|emb|CAH34943.1| putative type I restriction enzyme specificity protein
           [Burkholderia pseudomallei K96243]
          Length = 429

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 126/449 (28%), Positives = 203/449 (45%), Gaps = 67/449 (14%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESG------- 59
           Y +YKDSGV W+G +P HW V  +K           ESG  +  I   D  +G       
Sbjct: 6   YAKYKDSGVPWLGQVPTHWLVQRLKEVIAF-----IESGVSVNAI---DTPAGEGEPGVL 57

Query: 60  ------TGKYLPKDGN-SRQSDTSTVSIFAK-GQILYGKLG-PYLRKAIIADFDGICSTQ 110
                 +G++ P +       +   V+   K G ++  ++  P L  A      G+    
Sbjct: 58  KTSCVYSGEFTPSENKLVVPEELGRVACPVKAGTVIVSRMNTPDLVGA-----SGVVRQN 112

Query: 111 FLVL---------QPKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPM 159
           +  L           K+  PE +  W  +     ++E+ C G  ++M +       +  +
Sbjct: 113 YANLYLPDRLWQVHFKNACPEFVHYWSQTHSYRAQVESACAGTSSSMKNLSQDEFRSFIL 172

Query: 160 PIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKD 219
           P+PP +EQ  I   +  ET +I+ LI E+ + + LL EK+QA +S  VT+GLNPD   KD
Sbjct: 173 PLPPPSEQSAIATFLKHETRKINALIAEQEKLLTLLAEKRQATISRAVTRGLNPDAPTKD 232

Query: 220 SGIEWVGLVPDHWEVKPF-FALVTELNRK--NTKLIESNILSLSYGNII---QKLETRNM 273
           SG+ W+  VP HW +KP   A+V +      +   +E NI  +S G I        T+  
Sbjct: 233 SGVAWLREVPAHWNLKPMKRAVVFQRGHDLPSEDRVEGNIPVVSSGGISGWHNAAATKGP 292

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYL 333
            +    Y T         +  F+ L+ D   L            +A   V+ H     YL
Sbjct: 293 TIVTGRYGT---------IGEFVLLEEDCWPL-----------NTALYTVQMHDNVPKYL 332

Query: 334 AWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
            ++++S     +  ++ S +   +   D+    V +PP +EQ  I   ++ E +++D L 
Sbjct: 333 WYMLQSLKHIFILNSLKSAV-PGVDRNDIHPAIVCLPPAEEQPAIVAFLDAEISKLDALR 391

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
              E++I LLKERRS+ IAAAVTG+ID+R
Sbjct: 392 ADAERAIDLLKERRSALIAAAVTGKIDVR 420


>gi|229198631|ref|ZP_04325333.1| hypothetical protein bcere0001_41580 [Bacillus cereus m1293]
 gi|228584913|gb|EEK43029.1| hypothetical protein bcere0001_41580 [Bacillus cereus m1293]
          Length = 440

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 126/449 (28%), Positives = 207/449 (46%), Gaps = 44/449 (9%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           YK Y Q+KDS V+WIG IP+HW+   IK+ + +   R SE   D  +  L   + G  K 
Sbjct: 3   YKQYKQHKDSSVEWIGEIPQHWE---IKKVSAIFEQR-SEKVSDKDFEPLSVTKMGILKQ 58

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK------ 117
           L     +  +D     +  K   +            ++ FDG  S    V++PK      
Sbjct: 59  LENVAKTDNNDNRKKVL--KNDFVINSRSDRKGSCGVSQFDGSVSLICTVIKPKTKNTYM 116

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI--I 175
           D    L +  + S +  +    I +   +    W     I +P PP  EQ  I   +  I
Sbjct: 117 DYYHHLFRNKMFSEEFYRWGRGIVDD--LWSTRWDEFKRILIPSPPYEEQKSIANYLNYI 174

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            ET  I+ LI  + + +  L++ +Q+L++  VT GLNP  KMKDSG+EW+G +P HWE+K
Sbjct: 175 YET--IENLINNKKQQMATLQQYRQSLITETVTCGLNPYAKMKDSGLEWIGQIPSHWEIK 232

Query: 236 PFFALVTELN-------RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP 288
               +   +         K     E  I  L   N +++ E  N  L   S E+ +++  
Sbjct: 233 KNKMITNSITVGIVITPSKYYIEGEGGIPCLRSLN-VKEGEIINTDLVYISNESNELLSK 291

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV---------KPHGIDSTYLAWLMRS 339
            +I       + D  S+R+       ++   Y            K   I+S +L +L+ S
Sbjct: 292 SKI------YEGDLVSIRTGDTGVTSVVPKEYDGANCIDLIIIRKSTKINSAFLCYLLNS 345

Query: 340 YDLCKVFYA--MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            ++ K  Y    G  ++Q    E  K   +  PP +EQ +I N ++++T  ID +++KI+
Sbjct: 346 -NVAKQQYRNLSGGAIQQHFNIEMAKNTYITYPPFEEQLEIVNYLDLKTTEIDSVIKKIK 404

Query: 398 QSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
           + I+LL++ R S I  AVTG+ID+R  ++
Sbjct: 405 EQIILLEKYRQSLIYEAVTGKIDVRSYTE 433


>gi|170680371|ref|YP_001746681.1| type I restriction modification DNA specificity domain-containing
           protein [Escherichia coli SMS-3-5]
 gi|170518089|gb|ACB16267.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli SMS-3-5]
 gi|323160768|gb|EFZ46703.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli E128010]
 gi|330908618|gb|EGH37137.1| type 1 restriction-modification system, specificity subunit S
           [Escherichia coli AA86]
          Length = 428

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 126/425 (29%), Positives = 209/425 (49%), Gaps = 42/425 (9%)

Query: 25  WKVVPIKR-FT---KLNTG-----RTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75
           W  VP KR FT   ++N G     R + + K +I   L+D++             + SD 
Sbjct: 16  WNSVPAKRLFTSSKEINQGMKESNRLALTMKGVINRSLDDLQG-----------LQSSDY 64

Query: 76  STVSIFAKGQILYGKLG----PYLRKAIIADFDGICSTQFLVLQP--KDVLPELLQGWLL 129
           S   IF K  +++  +        R  I+ +  GI S  ++ +      + P     +  
Sbjct: 65  SVYQIFEKDDLVFKLIDLENIKTSRVGIVHE-RGIMSPAYIRVSASSNSIYPRFYYWYFF 123

Query: 130 SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERI 189
           ++ +T  I     G    +     +  IP+P+  ++ Q  +   +  ET RID+LI E+ 
Sbjct: 124 ALYLTN-IYNKLGGGVRQNLTAGDLLEIPVPLIDISLQKQVSTFLDRETQRIDSLIEEKQ 182

Query: 190 RFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT 249
            FI+LLKEK+QAL+S++VTKGL P+V+M+DSGIEW+G VP HWEVK    + +      +
Sbjct: 183 TFIKLLKEKRQALISHVVTKGLYPNVEMQDSGIEWIGQVPKHWEVKKIKHICSNFMYGTS 242

Query: 250 KLIESNILSLSYGNI-IQKLETRNMGLKPESYETYQIVDPGEIVFRFIDL----QNDKRS 304
           +  + N   + Y  + I  +++ N+  +   Y     VD    +    D+     N   +
Sbjct: 243 Q--DCNQSDVGYPVLRIPNIKSTNVDFEDLKYANISDVDALTYLLSRGDILVIRTNGNPN 300

Query: 305 L--RSAQVMERG--IITSAYMAVKP-HGIDSTYLAWLMRSYDLCK--VFYAMGSGLRQSL 357
           L  +SA     G  +  S  + + P  G+D+++L   M S  + +   F +  S    +L
Sbjct: 301 LVGQSALFDSNGQYLFASYLIKLTPKQGVDTSFLVEAMNSLSVRQALTFQSRTSVGNYNL 360

Query: 358 KFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTG 417
               +    + +PPI EQ  ITN ++  T  ID+L+++ ++SI LLKE R+S I AAVTG
Sbjct: 361 SIPSLANTSIAIPPIDEQKTITNYLSAATINIDLLIQETDKSIDLLKEHRTSLINAAVTG 420

Query: 418 QIDLR 422
           +ID+R
Sbjct: 421 KIDVR 425



 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 97/231 (41%), Gaps = 45/231 (19%)

Query: 7   YP--QYKDSGVQWIGAIPKHWKVVPIKRFTKL----------------------NTGRTS 42
           YP  + +DSG++WIG +PKHW+V  IK                           N   T+
Sbjct: 205 YPNVEMQDSGIEWIGQVPKHWEVKKIKHICSNFMYGTSQDCNQSDVGYPVLRIPNIKSTN 264

Query: 43  ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIAD 102
              +D+ Y  + DV++ T  YL   G+     T+          L+   G YL       
Sbjct: 265 VDFEDLKYANISDVDALT--YLLSRGDILVIRTNGNPNLVGQSALFDSNGQYL------- 315

Query: 103 FDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWK----GIGNI 157
                ++  + L PK  V    L   + S+ V Q   A+   +  S  ++      + N 
Sbjct: 316 ----FASYLIKLTPKQGVDTSFLVEAMNSLSVRQ---ALTFQSRTSVGNYNLSIPSLANT 368

Query: 158 PMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            + IPP+ EQ  I   + A T+ ID LI E  + I+LLKE + +L++  VT
Sbjct: 369 SIAIPPIDEQKTITNYLSAATINIDLLIQETDKSIDLLKEHRTSLINAAVT 419


>gi|331666002|ref|ZP_08366896.1| type I restriction-modification system, S subunit [Escherichia coli
           TA143]
 gi|331057053|gb|EGI29047.1| type I restriction-modification system, S subunit [Escherichia coli
           TA143]
          Length = 467

 Score =  144 bits (363), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 125/468 (26%), Positives = 217/468 (46%), Gaps = 67/468 (14%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           +  Y+AYP+Y+DSG++W   +P +WK   ++  + +  G T    K++I    +  E+GT
Sbjct: 4   LNKYQAYPEYRDSGMEWCNELPLNWKKTKLRWLSNIFAGGTPS--KNVI----DYWENGT 57

Query: 61  GKYLPKDG-------------NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF--DG 105
             ++                 ++   + S+     KG ++    G    K ++A    + 
Sbjct: 58  VPWISSGAVNQGYIVEPSTYISNAALENSSAKWIPKGALVVALAGQGKTKGMVAQLGINT 117

Query: 106 IC--STQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
            C  S   +VL  K+     +  WL+S    Q I  +  G      + + +G+I  P P 
Sbjct: 118 TCNQSMAAIVLYKKN-QSRYIFWWLIS--NYQNIRNMAGGDLRDGLNLELLGDIQCPKPR 174

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
             E   I   +  ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPDV MKDSG+ 
Sbjct: 175 NDESSKIALFLDHETAKIDDLIEKQQQLIELLKEKRQAVISHAVTKGLNPDVPMKDSGLT 234

Query: 224 WVGLVPDHW----------EVKPFFA--------LVTELNRKNTKLIESNILSLSYGNII 265
            +G  P HW          E K  F         L +EL  +   ++            I
Sbjct: 235 GLGEAPSHWFKSKLANTGDETKGCFVNGPFGSDLLASELKEEGVPVV-----------YI 283

Query: 266 QKLETRNMGLKPESYETYQ--------IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIIT 317
           + ++      K   Y T+Q         +   +++F  +     +  +      +  +IT
Sbjct: 284 RDIKATGYNRKSTVYVTHQKAQQLEICKLSSNDVIFSKVGDPPGEACVYPKNEPD-AVIT 342

Query: 318 SAYMAVKPH--GIDSTYLAWLMRS-YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKE 374
              M V+ +    ++ ++A+L+ S +    +      G R+ +   D K    + PP+ E
Sbjct: 343 QDVMRVRVNKKTFNAHFIAYLLNSNFGRQTINNISIEGTRKRVSLGDFKTTKFIFPPLGE 402

Query: 375 QFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
              I N +N + A+ID+++ K  Q+I+L++ERR++ I+AAVTG+IDLR
Sbjct: 403 AQSIVNALNEKCAQIDLIIFKTNQAIMLIQERRTALISAAVTGKIDLR 450


>gi|119513480|ref|ZP_01632504.1| hypothetical protein N9414_06519 [Nodularia spumigena CCY9414]
 gi|119461860|gb|EAW42873.1| hypothetical protein N9414_06519 [Nodularia spumigena CCY9414]
          Length = 437

 Score =  144 bits (363), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 133/472 (28%), Positives = 208/472 (44%), Gaps = 96/472 (20%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTG------RTSESGKDIIYI-----GL 53
           K YP YKDSG+ W+G IP+HW++V    F     G         + G  ++ I     G 
Sbjct: 2   KRYPHYKDSGIDWLGDIPEHWEIVRFSNFINFQEGPGIMAADFKDYGVPLLRIHNLKPGF 61

Query: 54  EDVE----------SGTGKYLPKDGN----SRQSDTSTVSIF---AKGQILYGKLGPYLR 96
            D+E            T K+   + +    S  + T  VSI    A+G I Y        
Sbjct: 62  VDLERCNYLEPQKVEKTWKHFKLNEDDILISCSASTGLVSIVDKKAEGSIAY-------- 113

Query: 97  KAIIADFDGICSTQFLVLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGI 154
                       T  + L+P   ++  E ++  + S     +IE +  G T+ H     +
Sbjct: 114 ------------TGIIRLKPANSNICREFIKIIVASELFFTQIELLKTGTTIQHYGPTHL 161

Query: 155 GNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPD 214
             I +  PPL EQ  I   + ++   ID  I+ + R IELLKE+K A+++  VTKGLNP 
Sbjct: 162 RQIKITFPPLYEQKKIACFLDSKLEEIDKFISNKQRLIELLKEQKTAIINRAVTKGLNPH 221

Query: 215 VKMKDSGIEWVGLVPDHWEVKPF----FALVTELNRKNTKL------------IESNILS 258
             MK SGIEW+G +P HWEV       +  V + N+ N  L               +I  
Sbjct: 222 APMKPSGIEWLGDIPAHWEVTRAKHISYVFVPQRNKPNLNLNIGFPWITMEDITSPSISK 281

Query: 259 LSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITS 318
            ++G ++ +++  N G K        ++  G ++   +       S+ + QV    II  
Sbjct: 282 STFGYLVSEIDAMNAGSK--------LLPEGSVIASCVG-NFGLSSVNTLQV----IINQ 328

Query: 319 AYMAVKPHGIDSTYLAWLM---RSY-----DLCKVFYAMGSGLRQSLKFEDVKRLPVLVP 370
              A  P  I+  YL +L+   +SY     +   + Y   +G  +         LP+++P
Sbjct: 329 QLQAYIPIKINPYYLRYLIGISKSYFEQIANATTLAYVNQAGFAE---------LPIILP 379

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           P  EQ  I   I+ E   ID  +  IE+ I L+KE R++ I+ AVTG+ID+R
Sbjct: 380 PNDEQLAIVRNIDKELTTIDKAITTIEKEIELIKEYRTTLISEAVTGKIDVR 431


>gi|149373160|ref|ZP_01892029.1| type I restriction-modification system, S subunit [unidentified
           eubacterium SCB49]
 gi|149354262|gb|EDM42832.1| type I restriction-modification system, S subunit [unidentified
           eubacterium SCB49]
          Length = 438

 Score =  144 bits (363), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 126/449 (28%), Positives = 204/449 (45%), Gaps = 50/449 (11%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K Y  YKDSG++WIG IP+HW  V +K  +K+ +G T    K       E    GT  +L
Sbjct: 2   KTYETYKDSGIEWIGEIPEHWSSVSLKWISKIYSGGTPSKNKP------EYWSDGTIPWL 55

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYL-RKAII---------------ADFDGICS 108
              G   Q D +  S +   + L      ++  KAI+                 F+  C+
Sbjct: 56  -NSGTVNQGDITEPSEYITEEALANSSAKWIPEKAILIALAGQGKTKGMVAQTQFEATCN 114

Query: 109 TQFLVLQPKDVLPELLQGWLLSIDVT-QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
               ++ P    PEL +  L  +    Q I  +  G      + + IG+IP P+P   EQ
Sbjct: 115 QSLGIIVPS--YPELNRYLLFWLRKNYQNIRNLGGGDKRDGINLEMIGSIPTPLPTKKEQ 172

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I   +  +T  ID LI+E+   ++L +E+K AL++  VTKG+ PD K+K+SGIEW+G 
Sbjct: 173 TAITNYLDKKTTEIDQLISEKEELVQLYQEEKTALINQAVTKGIKPDAKLKNSGIEWLGE 232

Query: 228 VPDHWE---VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQ 284
           +P+ W    +K     +   + K+T    S +  L   NI    +   +    ES+   +
Sbjct: 233 IPEDWNSLRLKYLGNFINGYSFKSTDFKSSGVRVLKISNI----QHMAIDWSDESFIDEE 288

Query: 285 IVDPGEIVFRFIDLQND-----KRSLRSAQVM-------ERGIITSAYMAVKPHGIDSTY 332
             D  +  FR   LQND      R + S  +        E+ ++       +P    + +
Sbjct: 289 FYDT-KSGFRV--LQNDLVFALTRPIISTGIKVALMNFDEKILLNQRNSIFRPKTKMTKW 345

Query: 333 LAWLMRSYDLCKVFYAM--GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
           + +++ S    + F      +G + ++   D+  + + VP  +EQ  I   I  ETA+ID
Sbjct: 346 IYFILLSSRFVQEFDKRIDKTGQQPNISSNDIGEISIPVPTKEEQTKIVEHIEKETAKID 405

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
             + K E+ I LL E R+S I+  VTG+I
Sbjct: 406 TKIAKAEKYINLLTEYRTSLISEVVTGKI 434



 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 102/222 (45%), Gaps = 19/222 (8%)

Query: 2   KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTG 61
           K  K   + K+SG++W+G IP+ W  + +K       G + +S  D    G+  ++    
Sbjct: 214 KGIKPDAKLKNSGIEWLGEIPEDWNSLRLKYLGNFINGYSFKS-TDFKSSGVRVLKISNI 272

Query: 62  KYLPKDGNSRQ------SDTSTVSIFAKGQILYGKLGPYLRKAI---IADFDG--ICSTQ 110
           +++  D +          DT +     +  +++    P +   I   + +FD   + + +
Sbjct: 273 QHMAIDWSDESFIDEEFYDTKSGFRVLQNDLVFALTRPIISTGIKVALMNFDEKILLNQR 332

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQ----RIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
             + +PK  + + +   LLS    Q    RI+   +   +S  D   IG I +P+P   E
Sbjct: 333 NSIFRPKTKMTKWIYFILLSSRFVQEFDKRIDKTGQQPNISSND---IGEISIPVPTKEE 389

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           Q  I E I  ET +IDT I +  ++I LL E + +L+S +VT
Sbjct: 390 QTKIVEHIEKETAKIDTKIAKAEKYINLLTEYRTSLISEVVT 431


>gi|323160944|gb|EFZ46868.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli E128010]
          Length = 394

 Score =  143 bits (361), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 97/278 (34%), Positives = 155/278 (55%), Gaps = 14/278 (5%)

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVK 216
           IP+P+  ++ Q  +   +  ET RID+LI E+  FI+LLKEK+QAL+S++VTKGL P+V+
Sbjct: 116 IPVPLIDISLQKQVSTFLDRETQRIDSLIEEKQTFIKLLKEKRQALISHVVTKGLYPNVE 175

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI-IQKLETRNMGL 275
           M+DSGIEW+G VP HWEVK    + +      ++  + N   + Y  + I  +++ N+  
Sbjct: 176 MQDSGIEWIGQVPKHWEVKKIKHICSNFMYGTSQ--DCNQSDVGYPVLRIPNIKSTNVDF 233

Query: 276 KPESYETYQIVDPGEIVFRFIDL----QNDKRSL--RSAQVMERG--IITSAYMAVKP-H 326
           +   Y     VD    +    D+     N   +L  +SA     G  +  S  + + P  
Sbjct: 234 EDLKYANISDVDALTYLLSRGDILVIRTNGNPNLVGQSALFDSNGQYLFASYLIKLTPKQ 293

Query: 327 GIDSTYLAWLMRSYDLCK--VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINV 384
           G+D+++L   M S  + +   F +  S    +L    +    + +PPI EQ  ITN ++ 
Sbjct: 294 GVDTSFLVEAMNSLSVRQALTFQSRTSVGNYNLSIPSLANTSIAIPPIDEQKTITNYLSA 353

Query: 385 ETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            T  ID+L+++ ++SI LLKE R+S I AAVTG+ID+R
Sbjct: 354 ATINIDLLIQETDKSIDLLKEHRTSLINAAVTGKIDVR 391



 Score = 92.8 bits (229), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 92/166 (55%), Gaps = 3/166 (1%)

Query: 253 ESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME 312
           ESN L+L+   +I +      GL+   Y  YQI +  ++VF+ IDL+N K S R   V E
Sbjct: 3   ESNRLALTMKGVINRSLDDLQGLQSSDYSVYQIFEKDDLVFKLIDLENIKTS-RVGIVHE 61

Query: 313 RGIITSAYMAVKP--HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVP 370
           RGI++ AY+ V    + I   +  W   +  L  ++  +G G+RQ+L   D+  +PV + 
Sbjct: 62  RGIMSPAYIRVSASSNSIYPRFYYWYFFALYLTNIYNKLGGGVRQNLTAGDLLEIPVPLI 121

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
            I  Q  ++  ++ ET RID L+E+ +  I LLKE+R + I+  VT
Sbjct: 122 DISLQKQVSTFLDRETQRIDSLIEEKQTFIKLLKEKRQALISHVVT 167



 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 97/231 (41%), Gaps = 45/231 (19%)

Query: 7   YP--QYKDSGVQWIGAIPKHWKVVPIKRFTKL----------------------NTGRTS 42
           YP  + +DSG++WIG +PKHW+V  IK                           N   T+
Sbjct: 171 YPNVEMQDSGIEWIGQVPKHWEVKKIKHICSNFMYGTSQDCNQSDVGYPVLRIPNIKSTN 230

Query: 43  ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIAD 102
              +D+ Y  + DV++ T  YL   G+     T+          L+   G YL       
Sbjct: 231 VDFEDLKYANISDVDALT--YLLSRGDILVIRTNGNPNLVGQSALFDSNGQYL------- 281

Query: 103 FDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWK----GIGNI 157
                ++  + L PK  V    L   + S+ V Q   A+   +  S  ++      + N 
Sbjct: 282 ----FASYLIKLTPKQGVDTSFLVEAMNSLSVRQ---ALTFQSRTSVGNYNLSIPSLANT 334

Query: 158 PMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            + IPP+ EQ  I   + A T+ ID LI E  + I+LLKE + +L++  VT
Sbjct: 335 SIAIPPIDEQKTITNYLSAATINIDLLIQETDKSIDLLKEHRTSLINAAVT 385


>gi|331650479|ref|ZP_08351551.1| putative type I restriction-modification system, S subunit
           [Escherichia coli M605]
 gi|331040873|gb|EGI13031.1| putative type I restriction-modification system, S subunit
           [Escherichia coli M605]
          Length = 435

 Score =  143 bits (360), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 134/450 (29%), Positives = 213/450 (47%), Gaps = 63/450 (14%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           +  Y+AYP+Y+DSG++W   +P +WK   ++  + +  G T    K++I    +  E+GT
Sbjct: 4   LNKYQAYPEYRDSGMEWCNELPLNWKKTKLRWLSNIFAGGTPS--KNVI----DYWENGT 57

Query: 61  GKYLPKDG-------------NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF--DG 105
             ++                 ++   + S+     KG ++    G    K ++A    + 
Sbjct: 58  VPWISSGAVNQGYIVEPSTYISNAALENSSAKWIPKGALVVALAGQGKTKGMVAQLGINT 117

Query: 106 IC--STQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
            C  S   +VL  K+    +   WL+S    Q I  +  G      + + +G+I  P P 
Sbjct: 118 TCNQSMAAIVLYKKNQSRYIFW-WLIS--NYQNIRNMAGGDLRDGLNLELLGDIQCPKPR 174

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
             E   I   +  ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPDV MKDSG+E
Sbjct: 175 NDESSKIALFLDHETAKIDNLIEKQQQLIELLKEKRQAVISHAVTKGLNPDVPMKDSGVE 234

Query: 224 WVGLVPDHWEVK--PFFALVTELNRKNTKLIESNILSLS-----YGNIIQKLETRNMGLK 276
           W+G VP HW +    +FA     N K+   I SN +        YG           GL+
Sbjct: 235 WLGEVPKHWHICKLKWFA-----NLKSGDFITSNSIEPEGNYPVYG---------GNGLR 280

Query: 277 PESYETYQIVDPGEIVF---RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST-Y 332
              Y +Y     GE V    +     N   ++      E  ++      V P+    T +
Sbjct: 281 --GYYSY-FTHNGEYVLIGRQGALCGNINYAIGKFWASEHAVV------VTPNERAVTIW 331

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           L  L+R  +L +  Y++ S  +  L  E +  L + +PP +EQ +I   I+   +    L
Sbjct: 332 LGELLRIMNLNQ--YSV-SAAQPGLAVERITDLYIPIPPYQEQVNIGTYISKYISLDKKL 388

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           +E    +I LLKERR++ I+AAVTG+IDLR
Sbjct: 389 IEHSTDNIELLKERRTALISAAVTGKIDLR 418


>gi|315638759|ref|ZP_07893932.1| restriction endonuclease S subunit [Campylobacter upsaliensis JV21]
 gi|315481168|gb|EFU71799.1| restriction endonuclease S subunit [Campylobacter upsaliensis JV21]
          Length = 438

 Score =  143 bits (360), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 109/426 (25%), Positives = 204/426 (47%), Gaps = 22/426 (5%)

Query: 10  YKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK-----DIIYIGLEDVESGTGKYL 64
           YK SG++W+G IPKHW++  + + +    G   ES        I  I + D+++    Y 
Sbjct: 16  YKPSGIKWLGEIPKHWEICKLNKVSYFINGYAFESSHFDYSFSIPVIRIGDIQNDKIIYH 75

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICS-TQFLVLQPKDVLPEL 123
                  Q +     I+ +G I+    G    K  + + +      Q + +   D+  ++
Sbjct: 76  TCLMTKEQENLKNFMIY-RGDIVIALSGATTGKFAVCNSNKKAYINQRVAIIRSDI--KI 132

Query: 124 LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDT 183
           L+ +L +      I+ +C G+   +   K +GN  +P+PPL EQ  I E +  +  +I  
Sbjct: 133 LKYYLSTFGFVNYIDMLCNGSAQPNISTKEVGNFKIPLPPLQEQKEIAEFLDKKCEKIQN 192

Query: 184 LITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF------ 237
            I ++ + I LL+EKKQAL++ +VTKGLNP+++ K+SGI ++GL+P HWE+K        
Sbjct: 193 YIDKKQKLITLLQEKKQALINEVVTKGLNPNIEFKNSGIAYLGLIPHHWEIKKLKYVGKV 252

Query: 238 ---FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFR 294
                L  E  +  +        +L + N ++  +   M         Y+I     +V  
Sbjct: 253 VLGKMLCNEHQKGYSHCYYLKSKNLQWLN-VEVSQIEKMWFSEYEKSLYRIKKDDLLVSE 311

Query: 295 FIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLR 354
             ++   K  + + ++ E  I  S +        ++ +  +L  +Y    VF ++ S + 
Sbjct: 312 GGEV--GKTCIWNNELAECYIQNSVHKITLNKFNNAKFFLYLFFTYGKLGVFDSVVSRVS 369

Query: 355 -QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAA 413
              L  E +  + ++VPP++EQ  I N ++ +  +I+  +EK ++ I L+KE +++ I  
Sbjct: 370 IAHLVLEKLVNVDMVVPPLQEQKQIANFLDEKCEKINSAIEKTKRQIELIKEYKNTLINE 429

Query: 414 AVTGQI 419
           AV G+I
Sbjct: 430 AVCGRI 435


>gi|290512141|ref|ZP_06551508.1| restriction modification system DNA specificity domain-containing
           protein [Klebsiella sp. 1_1_55]
 gi|289775136|gb|EFD83137.1| restriction modification system DNA specificity domain-containing
           protein [Klebsiella sp. 1_1_55]
          Length = 431

 Score =  143 bits (360), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 128/445 (28%), Positives = 213/445 (47%), Gaps = 55/445 (12%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M  YKAYP+YKDSGV+W+G +P+ W V  +K    +  G+  +S           V++  
Sbjct: 1   MAKYKAYPEYKDSGVEWLGLVPESWTVCRLKNLATIKNGQDYKS-----------VQTDD 49

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           G   P  G+  Q   ++  ++ K  +L G+ G   +   I +      T +         
Sbjct: 50  G--YPVMGSGGQFTFASKFMYDKPSVLLGRKGTIDKPLYINEPFWTVDTMYYT------- 100

Query: 121 PELLQG----WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL-AEQVLIREKII 175
            EL +G    +L  + +T +         +     + + N    +P   +E+  I E + 
Sbjct: 101 -ELNEGFDAKYLHYLALTIQFSRYSTNTALPSMTQEHLSNYKFSVPKAESERKKITEFLD 159

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPDV MKDSG+EW+G VP+HWEV 
Sbjct: 160 LETAKIDNLIEKQQQLIELLKEKRQAVISHAVTKGLNPDVPMKDSGVEWLGEVPEHWEVS 219

Query: 236 PF--FALV------------TELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE 281
            F   +LV            T  N   +  +   +  ++  N I  L++ +  L  +  E
Sbjct: 220 KFGYISLVVRGGSPRPAGDPTLFNGDYSPWV--TVAEITKDNEIY-LDSTDTFLTKKGSE 276

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSAQVME-RGIITSAYMAVKPHGIDSTYLAWLMRSY 340
             ++   G ++     L N   +L   +++          +  +   ID  Y  + + + 
Sbjct: 277 QCRVFKAGTLL-----LSNSGATLGVPKILSIDANANDGVVGFELLNIDHEYAYFYLSTL 331

Query: 341 DL-CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK--IE 397
               +     GSG + +L  E VK + + +PP  E   I + I  ET ++   +E   +E
Sbjct: 332 TTNLRESIKQGSG-QPNLNTEIVKSIAIPIPPENEIQRIVSFIK-ETIKLYSSIESGAME 389

Query: 398 QSIVLLKERRSSFIAAAVTGQIDLR 422
           Q + LL+ERR++ I+AAVTG+ID+R
Sbjct: 390 Q-VKLLQERRTALISAAVTGKIDVR 413


>gi|225026441|ref|ZP_03715633.1| hypothetical protein EUBHAL_00690 [Eubacterium hallii DSM 3353]
 gi|224956233|gb|EEG37442.1| hypothetical protein EUBHAL_00690 [Eubacterium hallii DSM 3353]
          Length = 408

 Score =  143 bits (360), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 78/214 (36%), Positives = 131/214 (61%), Gaps = 5/214 (2%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           + P+ +MKDSGIEW+G +P  W + P   + +E+  KNT L  +N  S  YG I+ K + 
Sbjct: 5   IRPETEMKDSGIEWIGDIPSSWTIFPANGVFSEVKEKNTDLKFTNAFSFKYGEIVDKKQV 64

Query: 271 RNM--GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP--H 326
            ++   LK E+  +Y IV    I+   ++L  D  S R A V E GIITSAY+A++P  +
Sbjct: 65  GDVDNNLK-ETLSSYTIVRKNTIMINGLNLNYDFVSQRVAIVNESGIITSAYLAIQPDEN 123

Query: 327 GIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVET 386
            I+  ++ +L++SYD  +VF+ +GSG+R++LK++D K++ ++ P + EQ  I + ++   
Sbjct: 124 KINPRFVLYLLKSYDYQQVFHGLGSGIRKTLKYQDFKKIMIVAPTLSEQQVIADYLDKTC 183

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           ++ID ++ + + SI   KE + S I  AVT  +D
Sbjct: 184 SQIDEIIAEAKASIYEYKELKQSVIFEAVTKGLD 217



 Score = 89.4 bits (220), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 110/235 (46%), Gaps = 18/235 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT---GKYLPKD 67
           KDSG++WIG IP  W + P             E   D+ +      + G     K +   
Sbjct: 12  KDSGIEWIGDIPSSWTIFPANGVF----SEVKEKNTDLKFTNAFSFKYGEIVDKKQVGDV 67

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYL----RKAIIADFDGICSTQFLVLQPKD--VLP 121
            N+ +   S+ +I  K  I+   L        ++  I +  GI ++ +L +QP +  + P
Sbjct: 68  DNNLKETLSSYTIVRKNTIMINGLNLNYDFVSQRVAIVNESGIITSAYLAIQPDENKINP 127

Query: 122 ELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
             +   L S D  Q    +  G   T+ + D+K    I +  P L+EQ +I + +     
Sbjct: 128 RFVLYLLKSYDYQQVFHGLGSGIRKTLKYQDFK---KIMIVAPTLSEQQVIADYLDKTCS 184

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
           +ID +I E    I   KE KQ+++   VTKGL+ +V+MKDSG+ W+G +P  WE+
Sbjct: 185 QIDEIIAEAKASIYEYKELKQSVIFEAVTKGLDKNVEMKDSGVYWIGKIPLDWEI 239



 Score = 39.7 bits (91), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 89/201 (44%), Gaps = 24/201 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-SESGKDIIYIGLEDVESGTGKYLPKDGN 69
           KDSGV WIG IP  W+++  K   K+  G   S  GK  +Y          G+Y  K+G 
Sbjct: 223 KDSGVYWIGKIPLDWEIIKTKYVIKIENGSNPSTEGKIPVYGSGAKSFKTCGEY--KEG- 279

Query: 70  SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLL 129
                  TV +  KG  L+    P+  +    + D    T F  + P +   EL   + +
Sbjct: 280 ------PTVLLGRKGATLH---IPHYIEGKYWNVD----TAFNTI-PINNKIELKYFYYV 325

Query: 130 S--IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITE 187
           +   D  + I        M+  +++   NI MP P +  Q  + + +  +   +D+LI+E
Sbjct: 326 ASCFDYNKYISQTTLPG-MTQTNYR---NIYMPYPSITIQEELVKWLDNKIFELDSLISE 381

Query: 188 RIRFIELLKEKKQALVSYIVT 208
           +   I  L+  K++L+  +VT
Sbjct: 382 KESLINDLEAYKKSLIYEVVT 402


>gi|257064600|ref|YP_003144272.1| hypothetical protein Shel_19070 [Slackia heliotrinireducens DSM
           20476]
 gi|256792253|gb|ACV22923.1| hypothetical protein Shel_19070 [Slackia heliotrinireducens DSM
           20476]
          Length = 425

 Score =  143 bits (360), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 112/430 (26%), Positives = 198/430 (46%), Gaps = 22/430 (5%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL-P 65
           Y  YKDSGV+WIG IP  W +   K           +   +   + L    +  G  L  
Sbjct: 4   YEAYKDSGVEWIGEIPSTWTLARTKAVFSSKKRVVGDKANEYQRLAL----TMHGVLLRD 59

Query: 66  KDGNS--RQSDTSTVSIFAKGQILYGKL---GPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           KD N   +        I    ++++  +        +  ++ + GI S  ++ L   D  
Sbjct: 60  KDDNEGLQPEQFEGYQILEANELVFKLIDLENIKTSRVGLSPYTGIVSPAYITLTQTDSD 119

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
                 W  ++        +      S  +   + N+PM +P   EQ  I   + A T  
Sbjct: 120 NRYFYYWFFALYQQNVFNQLGGNGVRSALNKDDLLNLPMLLPKQDEQRAIANYLDARTAE 179

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID L+ +  R  ELL+E ++A++S  VTKGL+PD  MKDSG+EW+G +P+ W V+P   L
Sbjct: 180 IDALVADCEREAELLREYRKAVISEAVTKGLDPDAPMKDSGVEWIGEIPEGWLVRPSKTL 239

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQ----KLETRNMGLKPESYETYQIVDPGEIVFRFI 296
             E         E    +  YG I Q     +E + M +  ++ + ++ V+PG+ V   I
Sbjct: 240 FAEAKELRHSDDEQCAATQKYGIIPQARYIAIENQRMVVADKNLDAWKHVEPGDFV---I 296

Query: 297 DLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLR- 354
            L++ +  L  +++   G +T  Y+ +K +  +++ Y  +L ++    +      + +R 
Sbjct: 297 SLRSFQGGLELSEIT--GCVTWHYIVLKGNDLVEAGYFKYLFKTTKYIESLQRTCTYIRD 354

Query: 355 -QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAA 413
            Q L++ +  ++P+ +P  +EQ  I   ++ +TA ID L+E  +     L+E R S I+ 
Sbjct: 355 GQDLRYSNFVQVPLPLPSREEQVAIGVYLDAKTAEIDALIEAKQTMADKLREYRKSLISE 414

Query: 414 AVTGQIDLRG 423
           AVTG+  + G
Sbjct: 415 AVTGKFKVPG 424


>gi|302345454|ref|YP_003813807.1| type I restriction modification DNA specificity domain protein
           [Prevotella melaninogenica ATCC 25845]
 gi|302149142|gb|ADK95404.1| type I restriction modification DNA specificity domain protein
           [Prevotella melaninogenica ATCC 25845]
          Length = 428

 Score =  143 bits (360), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 131/453 (28%), Positives = 204/453 (45%), Gaps = 59/453 (13%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIK-----RFTKLNTGRTSESGKDIIYIGLEDVESG 59
           K Y +YKDS VQW+G +P HW    IK      F+ +          D++   + D +  
Sbjct: 2   KRYGKYKDSAVQWLGKVPSHWNYSRIKFGLKSSFSGVWGDDEKGDDNDVVCYRVADFDYK 61

Query: 60  TGKYLPKDGNSRQSDTSTVSIFAKGQIL----------YGKLGPYLRKAIIADFD--GIC 107
            G    +    R  D  T   F + +IL           G + P + +A+IA+ D    C
Sbjct: 62  NGGLSEEKITIRNIDEKT---FKEREILPNDILIEKSGGGDVNP-VGRAVIANLDHKATC 117

Query: 108 STQFLVLQPKDVL--PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP----- 160
           S     ++  + +    LL  +  SI V Q++  +    T       GI N+ +P     
Sbjct: 118 SNFIHCVRCNENVLNTRLLYYFFYSIYV-QKVNLLFFNQTT------GIQNLKVPEYLGQ 170

Query: 161 ---IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKM 217
              +PPL+EQ  I   + A+T  ID +I +R + I LL+E K A++S  VTKGLNP+ KM
Sbjct: 171 VMFLPPLSEQQSIASFLDAKTKPIDDIIAKREQQIALLEEMKSAIISRAVTKGLNPEAKM 230

Query: 218 KDSGIEWVGLVPDHWEVKPFFALV-TELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           KDSGIEW+G VP++W +  F  L        +T+  E +     Y               
Sbjct: 231 KDSGIEWIGEVPENWNLLRFRLLCRISTGDSDTQDAEPDGEYPFYVR------------S 278

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQ----VMERGIITSAYMAVKPHGIDSTY 332
           P+   + +    G+ +    D     R          V +R  I + +  V    +DS Y
Sbjct: 279 PQVERSSKFTCEGDAILMAGDGAGAGRVFHHVDGKYAVHQRVYIFNQFNKV----VDSNY 334

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           L   MR     ++          S++   ++   V +P I EQ  IT+ ++ ETA+IDV 
Sbjct: 335 LYQFMRIMFPQRMNMGSAQSTVPSVRLHMIQNFVVPIPSIDEQRTITSYLDTETAKIDVR 394

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQIDLRGES 425
           ++K  + I LL+E + + I  AVTG+ID+RG S
Sbjct: 395 IDKRRKQIALLQEYKQALITDAVTGKIDVRGFS 427


>gi|261211183|ref|ZP_05925472.1| possible type I restriction-modification system S subunit [Vibrio
           sp. RC341]
 gi|260839684|gb|EEX66295.1| possible type I restriction-modification system S subunit [Vibrio
           sp. RC341]
          Length = 469

 Score =  142 bits (358), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 124/464 (26%), Positives = 218/464 (46%), Gaps = 51/464 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT--SESGKD--IIYIGLEDV 56
           M  Y+AYP+YKDS + W+  IP HW    ++       G T   E+ +D  I  +   +V
Sbjct: 1   MSKYQAYPEYKDSEIDWLETIPAHWLTSKLRYTFSFGKGLTITKENLRDTGIPCVSYGEV 60

Query: 57  ESGTG------KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKA-----IIADFDG 105
            S  G      ++  K        TS  ++  KG I++      +  +     ++++   
Sbjct: 61  HSKYGFEIDPARHPLKCVGDDYLKTSPYALLKKGDIVFADTSEDIDGSGNFTQLVSNEQV 120

Query: 106 ICSTQFLVLQPKDVLPELLQGWLL-SIDVTQRIEAICEGA---TMSHADWKGIGNIPMPI 161
                 ++ +P +        +LL S ++  +I    +G    +++ A  +G+    + +
Sbjct: 121 FAGYHTIIARPYNHECSRFYAYLLDSKELRTQIRHAVKGVKVFSITQAILRGVN---IWL 177

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           PPL E+  I   +  ET +IDTLI ++ + I+LLKEK+QA+VS+ VTKGLNP   MKDSG
Sbjct: 178 PPLKERNQIANFLDHETAKIDTLIEKQQQLIKLLKEKRQAVVSHAVTKGLNPQAPMKDSG 237

Query: 222 IEWVGLVPDHWEVKPFFALVTELNR---KNTKLIESNILSLSYGNIIQKLETR-NMGLKP 277
           +EW+G VP+HW + P    V  +N     +    +  +  +  GNI  K   + ++ L  
Sbjct: 238 VEWLGEVPEHWSISPLKHHVNTVNGFGFSSNNFQDEGVPFIRAGNIKNKTIVKPDIHLPQ 297

Query: 278 ESYETYQ--IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAW 335
              + YQ  I++ GE+V   I +      ++++ V + G++  +     P    +  +  
Sbjct: 298 AVVDKYQRVILNDGELV---ISMVGSDPKIKASAVGQVGLVPPSLAGSVP----NQNVVI 350

Query: 336 LMRSYDLCK--VFYAM-GSGLRQSLKFEDVKR-------------LPVLVPPIKEQFDIT 379
           L     L K  +FY + G+  R  L     K                   P + EQ +I 
Sbjct: 351 LREQSSLLKKFLFYVVCGTPYRHHLDVFSHKLANQSIISSSLIICAQFTFPELDEQKEIV 410

Query: 380 NVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           + ++ +  + D L+EK  +SI  + ER+++ I+A VTG+ID+R 
Sbjct: 411 DFLDTQLRKYDWLMEKATRSIEFMNERKTALISATVTGKIDVRN 454


>gi|261345477|ref|ZP_05973121.1| putative type I restriction-modification system specificity subunit
           [Providencia rustigianii DSM 4541]
 gi|282566524|gb|EFB72059.1| putative type I restriction-modification system specificity subunit
           [Providencia rustigianii DSM 4541]
          Length = 435

 Score =  142 bits (358), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 124/437 (28%), Positives = 198/437 (45%), Gaps = 34/437 (7%)

Query: 7   YPQYKDSGVQWIGAIPKHWKV---------VPIKRFTKLNT-GRTSESGKDIIYIGLEDV 56
           Y QY DSG +WIG IP HW +         V +K   +L     T E G  +I   ++D 
Sbjct: 10  YDQYIDSGYEWIGEIPLHWDLGKLGSCLFPVSVKNCPELPLLSITREQG--VIERDVDDQ 67

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ- 115
           ES    ++P        D S      KGQ    K+  +     ++ F GI S  + V   
Sbjct: 68  ES-NHNFIP-------DDLSGYKKLEKGQFGMNKMKAWQGSYGVSKFTGIVSPAYFVFDF 119

Query: 116 PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAEQVLIREK 173
            K + PE     + S        +  +G  +   D     +  IP  +P   EQ LI   
Sbjct: 120 TKAINPEFFNWAIRSKLYVSFFGSASDGVRIGQWDLSKTRMKVIPFVLPSEEEQSLIANF 179

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  +T  ID  I+ + + I LLKE+KQ ++   VT+GL+P+V MKDSG++W+G +P HWE
Sbjct: 180 LDKKTALIDEAISIKEQQISLLKERKQIIIQQAVTQGLDPNVPMKDSGVDWIGKIPAHWE 239

Query: 234 VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVF 293
           VK     VT++ ++       ++LS++   I  K      G     Y  YQIV  G+   
Sbjct: 240 VKR-LKYVTKILKRIIGYEGPDVLSITQKGIKVKDIESGEGQLSMDYSKYQIVRVGDFAM 298

Query: 294 RFIDLQNDKRSLRSAQVMERGIITSAYMAV--KPHGIDSTYLAWLMRSYDLCKVFYAMGS 351
             +DL      +   +    G+++  Y       +G+   +L  + +     K+FY  G 
Sbjct: 299 NHMDLLTGYVDISQFE----GVVSPDYRVFINTYNGLRDDFLLSIFQLGYQQKIFYRYGQ 354

Query: 352 GL----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
           G+    R     ++     + VPPI+EQ +I   +  E  ++D  +E +   I  LKE +
Sbjct: 355 GVSLLGRWRFPADNFNNFFIPVPPIEEQAEIVQSVQREWLKLDNAIELLISQIEKLKEYK 414

Query: 408 SSFIAAAVTGQIDLRGE 424
           ++ I +AVTG+I +  E
Sbjct: 415 TTLINSAVTGKIKITPE 431


>gi|148653129|ref|YP_001280222.1| restriction modification system DNA specificity subunit
           [Psychrobacter sp. PRwf-1]
 gi|148572213|gb|ABQ94272.1| restriction modification system DNA specificity domain
           [Psychrobacter sp. PRwf-1]
          Length = 431

 Score =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 127/439 (28%), Positives = 209/439 (47%), Gaps = 45/439 (10%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIK-RFTKLNTGRTSESGKDIIYIGLEDVESGTGK 62
           YKAYP+YK SGV+W+G IP+HW ++  K RF  L     +    D + + +  V     +
Sbjct: 12  YKAYPEYKGSGVEWLGEIPRHWGLLRGKWRFKSLKEVNRNLQCMDRLALTMRGV---IER 68

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYG--KLGPYLRKAIIADFD-GICSTQFLVLQP-KD 118
            +  D   + S  +   IF K  +++    L  Y    +   F  GI S  ++ L+P K 
Sbjct: 69  SIDSDDGLQPSAFTGYQIFEKDDLVFKLIDLENYKTSRVGLVFKKGIMSPAYIRLKPNKG 128

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           +L +    +   + +      I      S  +   +  I + +P   EQ  I + +  ET
Sbjct: 129 MLSKFFYYFYFDLYLRGIYNQIGGQGVRSALNASDLLEIEICVPSREEQAEIADFLDYET 188

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +IDTLI ++ R IELL EK+QA +S+ VTKGLNPDV MKDSG+EW+G VP HWEVK   
Sbjct: 189 AKIDTLIKKQQRLIELLTEKRQATISHAVTKGLNPDVPMKDSGVEWLGEVPAHWEVKDIK 248

Query: 239 ALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDL 298
             +  LN +                    + +++ G +   Y  Y       ++    D 
Sbjct: 249 FQLKSLNSRRI-----------------PINSQDRGDREGIYRYY---GASGVIDYIDDY 288

Query: 299 QNDKRSLRSAQVMERGIITSAYMAVKPHG---IDSTYLAWLMRSYDLCKVFYA------- 348
             D+ ++   +     +  S  +A   HG   +++   A ++ + D    F+A       
Sbjct: 289 IFDEPTVLVGEDGANLLSRSTPLAFSAHGKYWVNNH--AHILEAKDGLADFWAEVIDIID 346

Query: 349 ---MGSGLRQ-SLKFEDVKRLPVLVPP-IKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
              + +G  Q  L  E +  L +  PP IKE+ +I + I+    +   L+   +++I L+
Sbjct: 347 VTPLVTGSAQPKLTAEALSNLKIAFPPTIKERKEIESFIHSSKYKYGELIGYAKKAIQLM 406

Query: 404 KERRSSFIAAAVTGQIDLR 422
           +ERR++ I+AAVTG+ID+R
Sbjct: 407 QERRTALISAAVTGKIDVR 425


>gi|86153318|ref|ZP_01071522.1| type I restriction modification DNA specificity domain protein
           [Campylobacter jejuni subsp. jejuni HB93-13]
 gi|121613222|ref|YP_001000445.1| type I restriction modification DNA specificity domain-containing
           protein [Campylobacter jejuni subsp. jejuni 81-176]
 gi|167005388|ref|ZP_02271146.1| type I restriction modification DNA specificity domain protein
           [Campylobacter jejuni subsp. jejuni 81-176]
 gi|57790397|gb|AAW56129.1| Cj81-057 [Campylobacter jejuni subsp. jejuni 81-176]
 gi|85843044|gb|EAQ60255.1| type I restriction modification DNA specificity domain protein
           [Campylobacter jejuni subsp. jejuni HB93-13]
 gi|87249367|gb|EAQ72327.1| type I restriction modification DNA specificity domain protein
           [Campylobacter jejuni subsp. jejuni 81-176]
 gi|107770374|gb|ABF83711.1| putative type I restriction-modification system HsdS subunit
           [Campylobacter jejuni subsp. jejuni 81-176]
          Length = 422

 Score =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 112/433 (25%), Positives = 209/433 (48%), Gaps = 38/433 (8%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGL-------EDVESGTG 61
            +KDSG++W+G IP+HWK++  K F  L +    +       + L        D+ +  G
Sbjct: 3   NFKDSGIEWLGEIPEHWKLIKCKNFFVLKSIPIGDLWNKTKLLSLTLNGVIERDINNPEG 62

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYG--KLGPYLRKAIIADFDGICSTQFLVLQPKDV 119
           K+         SD ST  I  +G +++    +    R   ++  +G+ ++ + + + K+ 
Sbjct: 63  KF--------PSDFSTYQIVKEGDLIFCLFDVAETPRTIGLSKLNGMITSAYTIFEIKNQ 114

Query: 120 LPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
               L+ + + +D  + ++ +  G   T+S  D   + N+ +P+PPL EQ  I   +  +
Sbjct: 115 EKRFLEYFFIDLDNRKNLKFLYRGLRNTISKED---LLNLKIPLPPLKEQEQIANFLDEK 171

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF 237
             +I   I ++ + I LLKE+KQA ++   TKGL+ +V  KDSGIE++G +P HW++   
Sbjct: 172 CEQIKNFIEKKEKLITLLKEQKQAFINKATTKGLDKNVNFKDSGIEYLGEIPQHWKLVRL 231

Query: 238 FALV-----TELNRKNTKLIE-SNILSLSYGNI---IQKLETRNMGLKP-ESYETYQIVD 287
             ++     T  +  N K  +   I+ ++ G++     K   R +     + Y   +I D
Sbjct: 232 GLILKTSSGTTPDSGNDKYYKGGQIVWINSGDLNDGFLKDSKRKITQDALDDYSVLKIFD 291

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFY 347
              ++         K ++         +  +  +  K    ++ YL +L   Y   K   
Sbjct: 292 KDSLIIAMYGATIGKTAILKVNAC---VNQACCVLEKSAWYNTFYLFYLFNRYK--KELI 346

Query: 348 AMGSGLRQSLKFED-VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
           +MGSG  Q    +D +K L + +PP+KEQ  I N ++ +  +ID+L+EK E+ I L+KE 
Sbjct: 347 SMGSGGGQPNISQDIIKNLKIPLPPLKEQEQIANFLDEKCKKIDLLIEKTEKQIKLIKEY 406

Query: 407 RSSFIAAAVTGQI 419
           +++    AV G+I
Sbjct: 407 KTTLTNQAVCGRI 419



 Score =  110 bits (276), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 68/211 (32%), Positives = 113/211 (53%), Gaps = 15/211 (7%)

Query: 217 MKDSGIEWVGLVPDHWEV---KPFFAL----VTELNRKNTKLIESNILSLSYGNIIQKLE 269
            KDSGIEW+G +P+HW++   K FF L    + +L  K      + +LSL+   +I++  
Sbjct: 4   FKDSGIEWLGEIPEHWKLIKCKNFFVLKSIPIGDLWNK------TKLLSLTLNGVIERDI 57

Query: 270 TRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGID 329
               G  P  + TYQIV  G+++F   D+    R++  +++   G+ITSAY   +    +
Sbjct: 58  NNPEGKFPSDFSTYQIVKEGDLIFCLFDVAETPRTIGLSKL--NGMITSAYTIFEIKNQE 115

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
             +L +     D  K    +  GLR ++  ED+  L + +PP+KEQ  I N ++ +  +I
Sbjct: 116 KRFLEYFFIDLDNRKNLKFLYRGLRNTISKEDLLNLKIPLPPLKEQEQIANFLDEKCEQI 175

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
              +EK E+ I LLKE++ +FI  A T  +D
Sbjct: 176 KNFIEKKEKLITLLKEQKQAFINKATTKGLD 206


>gi|281355061|ref|ZP_06241555.1| putative type I site-specific restriction-modification system, S
           subunit [Victivallis vadensis ATCC BAA-548]
 gi|281317941|gb|EFB01961.1| putative type I site-specific restriction-modification system, S
           subunit [Victivallis vadensis ATCC BAA-548]
          Length = 430

 Score =  141 bits (356), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 115/435 (26%), Positives = 201/435 (46%), Gaps = 34/435 (7%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPI-KRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           K Y +YKDSG+ WIG +P+ WK+ P    FT ++   T +S ++++ + L+       + 
Sbjct: 2   KRYVKYKDSGIPWIGEVPEGWKICPFFAIFTPISI--TGKSVEELLSVYLDVGVVRFSEK 59

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPEL 123
             K  N+  +D S       G  +      +     I+ + GI S  +LV++    +   
Sbjct: 60  REKRANATSADMSKYQYVDIGDFVLNNQQAWRGSVGISQYKGIVSPAYLVMKTSKQINSS 119

Query: 124 LQGWLL---SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
              +L+   +      + +   G+   +  W  +    M  PPL EQ  I E + +   +
Sbjct: 120 FANYLVRSPACVYAYFLSSRGVGSIQRNIYWDELKRYKMVFPPLDEQREIVEYLDSVVAK 179

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID  I E+   IE L   KQ+++++ VTKG+NP+ KMKDSGI W+G VP+HW        
Sbjct: 180 IDGYIAEKEAEIEKLGLLKQSVIAHAVTKGINPNAKMKDSGIPWIGEVPEHW-------- 231

Query: 241 VTELNRKN-----TKLIESN---ILSLSYGNIIQKLETRNMGLKPESYET--YQIVDPGE 290
             +L  KN      +++E++   I     G +  +   R  G   ES++   YQ + PG+
Sbjct: 232 -LQLRGKNIFTRMARVVEADDEVITCFRDGQVTLRKNRRTDGF-TESFKEIGYQGIRPGD 289

Query: 291 IVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST-YLAWLMRSYDLCKVFYAM 349
           +V   +D       +  +    +G  T  Y+ ++P G  S  Y A+L+R         ++
Sbjct: 290 LVIHQMDAFAGAIGVSDS----KGKGTPVYICLQPKGEQSNFYYAYLLREMARTGYIKSL 345

Query: 350 GSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
             G+R+     ++E   +L + +PP  EQ  I   I+ +   ID  +  + + I  LK  
Sbjct: 346 YRGIRERSSDFRYETFGKLLLPIPPADEQRAIVEFIDRKVKEIDGFISAVREQIEKLKLY 405

Query: 407 RSSFIAAAVTGQIDL 421
           +   I+  VTG+I +
Sbjct: 406 KQRLISDVVTGKIKV 420


>gi|206975754|ref|ZP_03236666.1| type I restriction-modification system specificity determinant
           [Bacillus cereus H3081.97]
 gi|206746216|gb|EDZ57611.1| type I restriction-modification system specificity determinant
           [Bacillus cereus H3081.97]
          Length = 434

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 124/447 (27%), Positives = 200/447 (44%), Gaps = 52/447 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKL---NTGRTSESGKDIIYIGLEDVESGTGKY 63
           YPQYK + ++W+  IP  W+   + ++        G+T E            VE G    
Sbjct: 3   YPQYKKTNLEWLENIPSEWEYGGLTKYLDSIVDYRGKTPEK-----------VEEGIFLV 51

Query: 64  LPKDGNSRQSDTSTVSIFAK---------------GQILYGKLGPYLRKAIIADFDGICS 108
             K+    Q D S    F K               G +L+    P    A +   D   +
Sbjct: 52  TAKNIKHGQIDYSLSQEFVKIEEYEEVMRRGLPEIGDVLFTTEAPLGEVANVDRIDIALA 111

Query: 109 TQFLVLQP-KDVLPEL-LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
            + +  +  ++VL    L+ W+ S      +     G+T +      + ++ + +P  +E
Sbjct: 112 QRIIKFRGIENVLDNYYLKYWIQSHGFQSNLRTFATGSTAAGIKASKLSSLQVLLPSYSE 171

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q  I   +  +   ID LIT++ + I LL+EK+Q+++   VTKGLNP+VKMKDS +EW+G
Sbjct: 172 QKQIVLFLDNKVHEIDGLITQKEQMISLLEEKRQSMIIEAVTKGLNPNVKMKDSSVEWIG 231

Query: 227 LVPDHWEVKPF---FALVTELNRKNTKLIES-NILSLSYGNIIQKLETRNMGLKPESYET 282
            +P+ W +K     F +     RK  +  E+  +LSL+   +  K      G   ESYE 
Sbjct: 232 EIPESWNIKKIKYKFDI-----RKVIQPTEAPTVLSLTQKGLKVKDLNDFSGQHAESYEK 286

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK---PHGIDSTYLAWLMRS 339
           YQ V+  + V   +DL          +    G+ +  Y   +   P      YL +    
Sbjct: 287 YQRVEIDDYVMNGMDLLTGYVDCAKFE----GVTSPDYRVFRLRYPEECHDYYLRYFQMC 342

Query: 340 YDLCKVFYAMGSGL----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           Y   K+FY  G G+    R  L+ +  K  P+  PPI EQF I+  ++V+   I+  ++ 
Sbjct: 343 Y-FAKIFYGHGQGVSHLGRWRLQTDVFKGFPIPEPPIDEQFAISKYLSVKEIEINEAIDM 401

Query: 396 IEQSIVLLKERRSSFIAAAVTGQIDLR 422
           I+  I  LK+ R S I  AVTG+ID+R
Sbjct: 402 IKVQIQNLKDYRQSLIYEAVTGKIDVR 428


>gi|86130625|ref|ZP_01049225.1| type I site-specific deoxyribonuclease [Dokdonia donghaensis
           MED134]
 gi|85819300|gb|EAQ40459.1| type I site-specific deoxyribonuclease [Dokdonia donghaensis
           MED134]
          Length = 444

 Score =  141 bits (355), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 123/441 (27%), Positives = 200/441 (45%), Gaps = 38/441 (8%)

Query: 7   YPQYKDSGVQWIGAIPKHWKV-------VPIKRFTKLNTGRTS-ESGKDIIYIGLEDVES 58
           Y  YKDSGV+W+G IP+HW++        P+      N    S    K +I   +E+ E 
Sbjct: 11  YDSYKDSGVEWLGEIPEHWQLGRLGSILNPVSSKNHPNETLLSITREKGVIVRDIEN-ED 69

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ-PK 117
               ++P        D +   +  KGQ    K+  +     ++ + GI S  +   +  K
Sbjct: 70  SNHNFIP-------DDLTGYKLLKKGQFGMNKMKAWQGSYGVSSYTGIVSPAYYTFEFTK 122

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAEQVLIREKII 175
           ++ P      + S           +G  +   D     +  IP+ +PPL EQ  I E + 
Sbjct: 123 EIEPRFFHIAIRSKMYVSFFGKASDGVRIGQWDLSKDRMKRIPLAVPPLPEQTAIAEFLD 182

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            +T +ID  I  + + I LLKE+KQ L+   VT+GL+  V +KDSG+EW+G +P+HW+VK
Sbjct: 183 DKTTKIDDAIGIKQQQINLLKERKQILIHKAVTRGLDDSVTLKDSGVEWIGEIPEHWKVK 242

Query: 236 PF---FALVTELNRKNTKLIESNILSLSYGNIIQK----LETRNMGLK--PESY---ETY 283
            F   F L   L      L E  +  ++YG I  K    ++T    LK   + Y    T 
Sbjct: 243 RFRYIFQLGKGLTITKENLKEEGVFCVNYGEIHSKYGFEVDTNIQQLKCVDDDYLESNTN 302

Query: 284 QIVDPGEIVFRFIDLQND-KRSLRSAQVMERGIITSAYMAV--KPH-GIDSTYLAWLMRS 339
            ++  G+ V  F D   D + S     +  +  I + Y  V  KP   I+S + A++  S
Sbjct: 303 ALIKEGDFV--FADTSEDIEGSGNFTYLKSKDEIFAGYHTVVAKPKFKINSRFFAYVFES 360

Query: 340 YDLCKVFYAMGSGLRQSLKFEDVKRLP-VLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
                       G++     + + + P V  P I+EQ +I + +++ T +I+  +   EQ
Sbjct: 361 QSFRNQIRTKVKGVKVYSVTQSILKEPNVWYPSIQEQREIVDFLDIGTRKIETAIGLKEQ 420

Query: 399 SIVLLKERRSSFIAAAVTGQI 419
            I  LKE + S I   VTG++
Sbjct: 421 EIEKLKEYKGSLINGVVTGKV 441



 Score = 74.7 bits (182), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 101/211 (47%), Gaps = 14/211 (6%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSY--GNIIQKLETR--NM 273
           KDSG+EW+G +P+HW++    +++  ++ KN       +LS++   G I++ +E    N 
Sbjct: 15  KDSGVEWLGEIPEHWQLGRLGSILNPVSSKNHP--NETLLSITREKGVIVRDIENEDSNH 72

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK-PHGIDSTY 332
              P+    Y+++  G+     +        + S      GI++ AY   +    I+  +
Sbjct: 73  NFIPDDLTGYKLLKKGQFGMNKMKAWQGSYGVSSYT----GIVSPAYYTFEFTKEIEPRF 128

Query: 333 LAWLMRSYDLCKVFYAMGSGLR---QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
               +RS      F     G+R     L  + +KR+P+ VPP+ EQ  I   ++ +T +I
Sbjct: 129 FHIAIRSKMYVSFFGKASDGVRIGQWDLSKDRMKRIPLAVPPLPEQTAIAEFLDDKTTKI 188

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           D  +   +Q I LLKER+   I  AVT  +D
Sbjct: 189 DDAIGIKQQQINLLKERKQILIHKAVTRGLD 219


>gi|300112915|ref|YP_003759490.1| type I restriction enzyme, S subunit [Nitrosococcus watsonii C-113]
 gi|299538852|gb|ADJ27169.1| type I restriction enzyme, S subunit [Nitrosococcus watsonii C-113]
          Length = 471

 Score =  140 bits (354), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 122/454 (26%), Positives = 210/454 (46%), Gaps = 58/454 (12%)

Query: 6   AYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLP 65
           +YP+YKDSGV W+  IP+ W      RF +          K++ Y    D+ S TG    
Sbjct: 5   SYPEYKDSGVPWLEKIPRRW------RFFR---------AKNVFYP--IDLRSKTGAEEL 47

Query: 66  KDGNSRQSDTS----TVSIFAK-----------GQILYGKLGPYLRKAIIADFDGICSTQ 110
              + R   TS     V++F             G ++   L  +++    + + GI ST 
Sbjct: 48  LSVSERHGVTSRKSVNVTMFQAASYQGYKLCWPGDLVINSLWAWMQGLGFSKYHGIISTA 107

Query: 111 FLVLQPK-------DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           + V +P+            LL+      ++  R + I         D      +P+ +P 
Sbjct: 108 YGVYRPRVRRVSDFRYFDYLLRSAAYKWELRVRSKGIWRSRYQLKDD--DFLKMPILLPE 165

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
             EQ  I   +  +T +I+  I  + R IELLKE+KQ +++  VT+GL+P+V++K SG+E
Sbjct: 166 AEEQTQIARFLDWKTAQINQFIRNKRRLIELLKEQKQNVINQAVTRGLDPNVRLKPSGVE 225

Query: 224 WVGLVPDHWEVKPFFALVT-----ELNRKNT----KLIESNILSLSYGNIIQKLETRNMG 274
           W+G +P HWE      +V+        R N+    K++   + ++S    I   E R + 
Sbjct: 226 WIGDIPAHWETTKLKRVVSFNPSKSETRANSADEEKVVFLPMENISVNGDIDCSEKRPLS 285

Query: 275 LKPESYETYQIVDPGEIVFRFID--LQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDST 331
              E +  +     G++V   I    +N K +         G  T+  + ++P   ID  
Sbjct: 286 ---EVWSGFTYFRRGDVVMAKITPCFENGKGAYLQGLETGFGFGTTELIVLRPLKAIDGA 342

Query: 332 YLAWLM--RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           +L +LM  + + L    Y  G+  +Q +  + VK  P+ +PPI+EQ +I   I  ++A I
Sbjct: 343 FLRFLMWTKQFLLLGEQYMTGAAGQQRIPLDFVKNYPIGLPPIEEQREILAHIQEKSAEI 402

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           D  + + ++ I L++E R+  I+  VTGQ+D+RG
Sbjct: 403 DQALTRAQREIELIREYRTRLISDVVTGQVDVRG 436


>gi|254410563|ref|ZP_05024342.1| hypothetical protein MC7420_3078 [Microcoleus chthonoplastes PCC
           7420]
 gi|196182769|gb|EDX77754.1| hypothetical protein MC7420_3078 [Microcoleus chthonoplastes PCC
           7420]
          Length = 430

 Score =  140 bits (354), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 118/443 (26%), Positives = 198/443 (44%), Gaps = 40/443 (9%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           +  Y +YKDSGV+W+G IP+HW+ +  K   +L T    ++  + +     D+     + 
Sbjct: 3   FPRYERYKDSGVEWLGQIPEHWETLRTKNIFRLITEAAPKNNDEELLSVYSDIGVKPRRE 62

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPEL 123
           L + GN + S T    I  KG ++  KL  ++    I+D+DG+ S  + VL+    +   
Sbjct: 63  LEERGN-KASTTDGYWIVKKGDVIVNKLLAWMGAIGISDYDGVTSPAYDVLRAYKPIDSK 121

Query: 124 LQGWLLSIDVT-----QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
              +L    +      Q    I E     + D    G I +P PP   Q  I E +  + 
Sbjct: 122 YYHYLFRSPICLSKLKQHSRGIMEMRLRLYFD--EFGRIRLPYPPFEIQKRIVEFLDRKC 179

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
             I+  I  + R IELL+E+K  L++  VTKGL+P+  MKDSGIEW+G +P HWEVK   
Sbjct: 180 GEIEDAIAHKKRLIELLEEQKTILINQAVTKGLDPNAPMKDSGIEWIGEIPTHWEVKKLK 239

Query: 239 AL-----VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVF 293
            +     V  +   +   +E  ++ L           R++ +KP        V   E   
Sbjct: 240 RISPCITVGIVITPSKYYVEEGVICL-----------RSLNIKPNKILVKDSVYISERSN 288

Query: 294 RFID----LQNDKRSLRSAQVMERGIITSAYMAV---------KPHGIDSTYLAWLMRSY 340
           +++        D   +R+ Q     ++   +            KP      +++  M S 
Sbjct: 289 KYLSKSKIFAGDIVCVRTGQPGVSAVVDRRFDGANCIDLIIIRKPKNDLPKFVSLAMNS- 347

Query: 341 DLCKVFYAMGS--GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
           ++C+  Y  G+   ++Q    E  + L + +PP+ EQ  I N I+        L+  I++
Sbjct: 348 EVCRSQYLTGASGAIQQHFNIEMAQNLVIAIPPLPEQIKIYNHISKIQKNTMDLMNFIKR 407

Query: 399 SIVLLKERRSSFIAAAVTGQIDL 421
            I L+ E +   IA AVTG+I +
Sbjct: 408 EIDLMNELKQILIAEAVTGKIKI 430


>gi|259156142|gb|ACV96090.1| type I restriction-modification protein [Providencia alcalifaciens
           Ban1]
          Length = 436

 Score =  140 bits (353), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 120/446 (26%), Positives = 207/446 (46%), Gaps = 51/446 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           + QY DSG +WIG IP+HW +V      KL +  +S S K+   + L  +    G  + +
Sbjct: 10  HGQYIDSGYEWIGEIPQHWDLV------KLGSCLSSVSVKNCPELPLLSITREQG-VIER 62

Query: 67  DGNSRQ-------SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ-PKD 118
           D + ++        D S      KGQ    K+  +     ++ F GI S  + V    K 
Sbjct: 63  DVDDQELNHNFIPDDLSGYKKLEKGQFGMNKMKAWQGSYGVSKFTGIVSPAYFVFDFTKA 122

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAEQVLIREKIIA 176
           + PE     + S        +  +G  +   D     +  IP  +P   +Q LI   +  
Sbjct: 123 IDPEFFNWAIRSKLYVSFFGSASDGVRIGQWDLSKTRMKVIPFVLPSEEDQSLIANFLAK 182

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           +T +I+  I  + + I LLKE+KQ ++   VT+GL+P+V MKDSG+ W+G +P HWEV  
Sbjct: 183 KTTQINDAIAIKEQQINLLKERKQIIIQQAVTQGLDPNVPMKDSGVNWIGKIPAHWEV-- 240

Query: 237 FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFI 296
                     + +K + +     ++ + +Q   T+  G+ P+  + Y+ +    +V   I
Sbjct: 241 ----------RRSKFVFTQRKERAWKDDVQLSATQAYGVIPQ--DQYEELTGKRVV--KI 286

Query: 297 DLQNDKR----------SLRSAQ-----VMERGIITSAYMAVKP-HGIDSTYLAWLMRSY 340
            L  DKR          S+RS Q        +G I S+Y+ ++    ID ++  +L++  
Sbjct: 287 QLHLDKRKHVEKDDFVISMRSFQGGLERAWSQGCIRSSYVVLRALEEIDPSFYGYLLKLP 346

Query: 341 DLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
                     S +R  Q L F++  ++ + +PPI+EQ +I N ++      D  +E +  
Sbjct: 347 SYIAALQQTASFIRDGQDLNFDNFSKVDLFIPPIEEQKEIANYVSAFMKSSDEGIELLLA 406

Query: 399 SIVLLKERRSSFIAAAVTGQIDLRGE 424
            I  LKE +++ I +AVTG+I +  E
Sbjct: 407 QIEKLKEYKTTLINSAVTGKIKITPE 432


>gi|56750493|ref|YP_171194.1| type I restriction-modification [Synechococcus elongatus PCC 6301]
 gi|56685452|dbj|BAD78674.1| type I restriction-modification [Synechococcus elongatus PCC 6301]
          Length = 453

 Score =  140 bits (352), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 127/476 (26%), Positives = 210/476 (44%), Gaps = 87/476 (18%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTGRTSESGKDIIYIGLEDVESG--- 59
           +  YP YKD G++W+  +P HW V+ ++R   ++ +G +  +       G+  V      
Sbjct: 3   FPRYPAYKDCGIEWLEKLPSHWNVLQLRRLIPEIESGVSVNALDHAPDEGIPSVLKTSCV 62

Query: 60  -TGKYLPKDGNSR-QSDTSTVSIFAK-GQILYGKLG-PYLRKAI---IADFDGI-CSTQF 111
            TG + P++     Q D    +   K G+++  ++  P L  A    + D+D +    + 
Sbjct: 63  YTGSFRPEERKEIIQEDIDRAACPVKSGRLIVSRMNTPDLVGAAGLSLVDYDCVFLPDRL 122

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVL 169
             ++  +V P     W  +     +++ +C G  ++M +       +  +P+P   EQ+ 
Sbjct: 123 WQVRISNVYPNFAYYWTQTQIYRDQVKMVCSGTSSSMQNLSQDNFLSFILPVPSDEEQIA 182

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  ET +ID LI E+ R I LL+EK+QA++S+ VTKGLNPD  +KDSGIEW+G VP
Sbjct: 183 IASFLDRETAKIDALIAEQQRLIALLQEKRQAVISHAVTKGLNPDAPLKDSGIEWLGQVP 242

Query: 230 DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET---YQIV 286
            HW+                            G I    +T + G  P + E    Y   
Sbjct: 243 AHWKT---------------------------GKIKHYFKTSSGG-TPNTEEQALYYADS 274

Query: 287 DPGEIVFRFIDLQNDKRSLRSAQVMERG---------------IITSAYMAVK------- 324
           D G    R  D++N +  +RSA+V                   ++ + Y           
Sbjct: 275 DSGIPWVRTTDIENQE--VRSAEVSITNQAIQDTACEILPVDTVLVALYGGGGTVGKNGI 332

Query: 325 ---PHGIDSTYLAWLMRSYDLCKVFY--------------AMGSGLRQSLKFEDVKRLPV 367
              P  I+    A L+ SY    +F               A+ +    ++  E V+    
Sbjct: 333 LTFPAAINQALCA-LLPSYYAVPMFTFRYIQFLRPFWMERAVSARKAGNISQELVRDTVF 391

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            +PP+ EQ  I   I+ +   I  L  +  +S+ LL+ERRS+ I+AAVTGQID+RG
Sbjct: 392 ALPPLDEQILIVKHIHSQLEEITSLENESTKSLSLLQERRSALISAAVTGQIDVRG 447


>gi|114563773|ref|YP_751286.1| restriction modification system DNA specificity subunit [Shewanella
           frigidimarina NCIMB 400]
 gi|114335066|gb|ABI72448.1| restriction modification system DNA specificity domain [Shewanella
           frigidimarina NCIMB 400]
          Length = 462

 Score =  139 bits (349), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 138/473 (29%), Positives = 225/473 (47%), Gaps = 76/473 (16%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG-------LED- 55
           YKAY +YKDSGV+W+  +P  W+V+ +K   K        +G + I IG       LED 
Sbjct: 5   YKAYSEYKDSGVEWLKLLPSTWQVLKVKFLLK--------NGSEGIKIGPFGSALKLEDM 56

Query: 56  VESGTGKYLPKDGNSR----------QSDTSTVSIFAK--GQILYGKLGPYLRKAII--- 100
           VE G   Y  ++   R          Q+    + ++    G IL   +G   +  ++   
Sbjct: 57  VEKGIRVYGQENIIKRDFTLGKRFISQTKYKDMKVYTAEAGDILITMMGTSGKCQVVPEN 116

Query: 101 ADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQ----RIEAICEGATMSHADWKGIG 155
           AD  GI  +  L L+    +LPEL +   L +D  Q    +I    +G+ M   +   + 
Sbjct: 117 ADL-GIIDSHLLKLRTNSKILPELFR---LLVDEAQEIKDQISKQGKGSIMLGLNSSIVK 172

Query: 156 NIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDV 215
            +  P+P + EQ  I   +  ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPD 
Sbjct: 173 ELEFPLPSIEEQTQILCFLDHETAKIDDLIAKQEKLIELLKEKRQAVISHAVTKGLNPDS 232

Query: 216 KMKDSGIEWVGLVPDHWEV----------------KPFFA-LVTE--LNRKNTKLIESNI 256
            MK+SG+ W+G VP+HW V                 PF + L +E  ++  +  +IESN 
Sbjct: 233 PMKNSGVVWLGEVPEHWVVCCLKHIKGKEKGSFVDGPFGSNLKSEHFVDDGDVYVIESNF 292

Query: 257 LSLSYGNIIQKLETRNMGLKPESYETYQIVDP--GEIVFRFIDLQNDKRSLRSAQVMERG 314
            +    +   KL+T ++      +ET    +   G I+   I  +    S+    +  + 
Sbjct: 293 ATTGMLD-TSKLKTISVA----HFETISRSETKEGAIILAKIGARYGMNSILPC-LPHKA 346

Query: 315 IITSAYMAVK--PHGIDSTYLAWLMRSYDLCKVFYAMGSGL----RQSLKFEDVKRLPVL 368
           +++   +++K     +D  Y   L+      K   AM  G+    + +L    +  LP L
Sbjct: 347 VVSGNCLSLKINEKTMDVLYCHQLLTHL---KQEGAMDDGVNVTAQPALSLGQLNNLPFL 403

Query: 369 VPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            PP KEQ +I + I        +L+ K  + I L KER+++ I+A +TG+ID+
Sbjct: 404 SPPQKEQSEIASFIQQRDESFSILINKAIKLIELSKERKTALISAVLTGKIDV 456


>gi|297619043|ref|YP_003707148.1| restriction modification system DNA specificity subunit
           [Methanococcus voltae A3]
 gi|297378020|gb|ADI36175.1| restriction modification system DNA specificity subunit
           [Methanococcus voltae A3]
          Length = 440

 Score =  139 bits (349), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 82/201 (40%), Positives = 114/201 (56%), Gaps = 5/201 (2%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           + KDSGV+WIG IP  W V  +K    L + +  E  K++ YIGLE +ES TGKY+    
Sbjct: 228 ELKDSGVEWIGQIPNDWDVKKLKYEVSLRSIK-GEYTKNLKYIGLEHIESSTGKYIK--- 283

Query: 69  NSRQSDTSTV-SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGW 127
           NS + +   + + F K  IL+GKL PYL K IIA+FDG+CS++ LVL  + +    L+  
Sbjct: 284 NSEELNIEGICNKFKKNDILFGKLRPYLAKCIIANFDGVCSSELLVLNTQRINNIFLKYV 343

Query: 128 LLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITE 187
           +L+      I +   GA M   +W  +GNI +P P + EQ  I   +  +T  ID LI  
Sbjct: 344 ILNSKFINYINSSTYGAKMPRTNWDFVGNIKIPHPNMQEQETISNFLDTKTEEIDNLINN 403

Query: 188 RIRFIELLKEKKQALVSYIVT 208
               IE LKE KQ+L+S  VT
Sbjct: 404 TKLQIEKLKEAKQSLISEAVT 424



 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 117/212 (55%), Gaps = 12/212 (5%)

Query: 216 KMKDSGIEWVGLVPDHWEV---KPFFALVTELNRK-NTKLIESNILSLSYGNIIQKLETR 271
           ++KDSG+EW+G +P  W++   K  F      N+K N + I  N+LSL+   +I +    
Sbjct: 11  ELKDSGVEWIGQIPKDWDIIKGKNIF-----YNKKVNNRGILKNVLSLTLNGVIDRDPMS 65

Query: 272 NMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV-KPHGIDS 330
           N GL+P+ ++ YQ  +   +VF+ IDL+N   S R     + G+++ AY+ +   + I  
Sbjct: 66  NEGLQPKDFKGYQEFEKNNLVFKLIDLENINTS-RVGITHKSGLMSPAYIRIINKYQICV 124

Query: 331 TYLAWLMRSYDLCKVFYAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
            Y  +   SY L K++  +G SG+R ++   D+  L VL    KEQ  I N ++++T  I
Sbjct: 125 KYYYYTYYSYYLKKIYNNLGNSGVRSAMNSCDLLNLEVLQTFEKEQEKIANFLDIKTEEI 184

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           + ++ K E+ I  L+E + S I+  VTG+  +
Sbjct: 185 ENIISKKEKLINKLEEAKKSLISEVVTGKFKI 216



 Score = 83.2 bits (204), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 109/457 (23%), Positives = 194/457 (42%), Gaps = 70/457 (15%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRF---TKLNTGRTSESGKDIIYIGLEDVESGT 60
           Y+   + KDSGV+WIG IPK W ++  K      K+N     ++   +   G+ D +  +
Sbjct: 6   YRKAEELKDSGVEWIGQIPKDWDIIKGKNIFYNKKVNNRGILKNVLSLTLNGVIDRDPMS 65

Query: 61  GKYL-PKDGNSRQS----------------DTSTVSIFAKGQILYGKLGP-YLRKAIIAD 102
            + L PKD    Q                 +TS V I  K     G + P Y+R  II  
Sbjct: 66  NEGLQPKDFKGYQEFEKNNLVFKLIDLENINTSRVGITHKS----GLMSPAYIR--IINK 119

Query: 103 FDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
           +  IC   +        L ++                +      S  +   + N+ +   
Sbjct: 120 YQ-ICVKYYYYTYYSYYLKKIYNN-------------LGNSGVRSAMNSCDLLNLEVLQT 165

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNP-DVKM---- 217
              EQ  I   +  +T  I+ +I+++ + I  L+E K++L+S +VT      DVK+    
Sbjct: 166 FEKEQEKIANFLDIKTEEIENIISKKEKLINKLEEAKKSLISEVVTGKFKIIDVKLIKRE 225

Query: 218 ----KDSGIEWVGLVPDHWEVKPFFALVTELN-----RKNTKLIESNILSLSYGNIIQKL 268
               KDSG+EW+G +P+ W+VK     V+  +      KN K I    +  S G  I+  
Sbjct: 226 KEELKDSGVEWIGQIPNDWDVKKLKYEVSLRSIKGEYTKNLKYIGLEHIESSTGKYIKNS 285

Query: 269 ETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER--GIITSAYMAVKPH 326
           E  N+      ++        +I+F  +      R   +  ++    G+ +S  + +   
Sbjct: 286 EELNIEGICNKFK------KNDILFGKL------RPYLAKCIIANFDGVCSSELLVLNTQ 333

Query: 327 GIDSTYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
            I++ +L +++ +        +   G +     ++ V  + +  P ++EQ  I+N ++ +
Sbjct: 334 RINNIFLKYVILNSKFINYINSSTYGAKMPRTNWDFVGNIKIPHPNMQEQETISNFLDTK 393

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           T  ID L+   +  I  LKE + S I+ AVTG+IDLR
Sbjct: 394 TEEIDNLINNTKLQIEKLKEAKQSLISEAVTGKIDLR 430


>gi|257791267|ref|YP_003181873.1| restriction modification system DNA specificity subunit
           [Eggerthella lenta DSM 2243]
 gi|257475164|gb|ACV55484.1| restriction modification system DNA specificity subunit
           [Eggerthella lenta DSM 2243]
          Length = 395

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 113/418 (27%), Positives = 198/418 (47%), Gaps = 33/418 (7%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           + KDSGV WIG +P +W++VPIK    +  G    +  DI   G     SG G+     G
Sbjct: 3   ETKDSGVDWIGEVPVNWEIVPIKADVSIGHGSDPTTPGDIPVWG-----SG-GEPFKTCG 56

Query: 69  NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWL 128
             +      V +  KG +   +L   L   +   FD   +++ L L+             
Sbjct: 57  EHKNG--PAVLLGRKGTLDCPQLVTGLYWNVDTAFDAKITSKKLSLK-------FFYYAA 107

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITER 188
             +D+   +    +  +M+  DW    N  +P PPLAEQ  I   +      ID  + +R
Sbjct: 108 TCVDIKPYMTNTAK-PSMTQFDWD---NSRIPRPPLAEQRRIISYLDERCAAIDEDVAKR 163

Query: 189 IRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKN 248
              I  LKE K++L+++ VTKGL+P+ +MKDSG++W+G VP +W +     +    + +N
Sbjct: 164 RDVIGKLKEYKKSLIAHAVTKGLDPNTEMKDSGVDWIGEVPANWRLTKIGQV---YDLRN 220

Query: 249 TKLIESNI--LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLR 306
           TK+ + +   LS++   I+ +L++     K ++++  ++V  G+ V   I+ ++D+R   
Sbjct: 221 TKVSDCDYEPLSVTMQGIVPQLDS---AAKTDAHDDRKLVMEGDFV---INSRSDRRGSC 274

Query: 307 SAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSL---KFEDVK 363
                +  +     + +    ++  +  WL  +      FY  G G+   L   K+ ++K
Sbjct: 275 GIARQDGSVSLINTVLIPREHMEPRFYDWLFHTTLFADEFYKNGHGIVDDLWTTKWAEMK 334

Query: 364 RLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            + ++ PP + Q  + N ++   A ID  + + EQ I  L E R S I  AVTG+ID 
Sbjct: 335 GITIVEPPFETQITVANYLDERCAAIDEAIARQEQLIEKLGEYRKSVIHHAVTGKIDC 392


>gi|120597918|ref|YP_962492.1| putative type I site-specific restriction-modification system, S
           subunit [Shewanella sp. W3-18-1]
 gi|120558011|gb|ABM23938.1| putative type I site-specific restriction-modification system, S
           subunit [Shewanella sp. W3-18-1]
          Length = 429

 Score =  137 bits (344), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 121/445 (27%), Positives = 207/445 (46%), Gaps = 56/445 (12%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT---GKY 63
           Y  YKDS   WIG +P+HW +  +K        R + S           + SG    GK 
Sbjct: 10  YQTYKDSTEGWIGDVPEHWDIRKLKHLFYEKKHRPNMS-----------LNSGAISFGKV 58

Query: 64  LPKDGNS-RQSDTSTVSIFAKGQILYGKLGP-----YLRKAIIADFDGICSTQFLVLQPK 117
           + KD      S  ++      G+ L   L        LR A+ ++ D + S  ++V++ K
Sbjct: 59  VTKDDEKILLSTKASYQEVLSGEFLINPLNLNYDLISLRIAL-SEIDVVVSAGYIVIKEK 117

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
           + L +    +LL       ++ +  G   +   +  I N  +  PPL EQ LI   +  +
Sbjct: 118 EELQKQYFKYLLHRYDVAYMKLLGSGVRQT-ISFNHIANSLLVFPPLEEQSLIANYLEKK 176

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF 237
           T ++D  I  + + I LLKE+KQ ++   VT+GL+P+V MKDSG++W+G VP HWEV   
Sbjct: 177 TAQVDEAIAIKEQQISLLKERKQIIIQQAVTQGLDPNVPMKDSGVDWIGKVPAHWEV--- 233

Query: 238 FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
                    + +K + +     ++ + +Q   T+  G+ P+  + Y+ +    +V   I 
Sbjct: 234 ---------RRSKFVFTQRKERAWKDDVQLSATQAYGVIPQ--DQYEELTGKRVV--KIQ 280

Query: 298 LQNDKR----------SLRSAQ-----VMERGIITSAYMAVKP-HGIDSTYLAWLMRSYD 341
              DKR          S+RS Q        +G I S+Y+ ++    ID ++  +L++   
Sbjct: 281 FHLDKRKHVEKDDFVISMRSFQGGLERAWSQGCIRSSYVVLRALDEIDPSFYGYLLKLPS 340

Query: 342 LCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
                    S +R  Q L F++  ++ + +PPI+EQ +I N ++      D  +E +   
Sbjct: 341 YIAALQQTASFIRDGQDLNFDNFSKVDLFIPPIEEQKEIANYVSAFMKSSDEGIELLFAQ 400

Query: 400 IVLLKERRSSFIAAAVTGQIDLRGE 424
           I  LKE ++S I +AVTG+I +  E
Sbjct: 401 IEKLKEYKTSLINSAVTGKIKITPE 425


>gi|189485041|ref|YP_001955982.1| type I restriction-modification system substrate-binding subunit
           [uncultured Termite group 1 bacterium phylotype Rs-D17]
 gi|170287000|dbj|BAG13521.1| type I restriction-modification system substrate-binding subunit
           [uncultured Termite group 1 bacterium phylotype Rs-D17]
          Length = 434

 Score =  136 bits (342), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 123/436 (28%), Positives = 211/436 (48%), Gaps = 32/436 (7%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +YK SG++WIG IPK+W  V  +        R ++  K+  Y+ L     G   Y  K
Sbjct: 4   YSKYKPSGIEWIGDIPKNWNFVSCRLIVSERNER-NKGMKNNNYLSLM-ANIGVIPYEEK 61

Query: 67  D--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELL 124
              GN +  +     I  +G ++   +  ++    I+ +DGICS  ++VL     + E  
Sbjct: 62  GDIGNKKPENLEKCKIVYEGDLIINSMNYFIGSYGISKYDGICSPVYIVLYANTKVIE-- 119

Query: 125 QGWLLSIDVTQRIEAICE---GATMSHA---DWKGIGNIPMPIPPLAEQVLIREKIIAET 178
             +   +    + + + +      + H    +W  + NI +P+P L EQ  I   +  +T
Sbjct: 120 PRFAFRVFENPKFQGVAQSFGNGILEHRRAINWDILKNIKIPVPLLEEQRNILSFLDKKT 179

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID LI+++ + I+LL+E +Q+++S  VTKGL+  V+MK SGIEW+G +P  W+V  F 
Sbjct: 180 EKIDALISDKEKLIKLLREYRQSIISETVTKGLDKKVQMKHSGIEWIGDIPYDWKVNKFN 239

Query: 239 ALV----TELN-RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP----- 288
            ++    T LN R N KL + +   ++  N  +     +      + E   I++      
Sbjct: 240 RIIIRVSTGLNPRNNFKLGDGDCYYVTIKNFKKGKLFLDEKCDRMTKEALNIINERSDLK 299

Query: 289 -GEIVFRFIDLQNDKRSLRSAQVMERGIITSAY-MAVKPHGIDSTYLAWLM--RSY--DL 342
             +I+F  I  +  +  L S       I  S + + V    +   +  +L+  +S+  DL
Sbjct: 300 IDDILFSSIG-EEAEAYLISEHPTNWNINESVFTIRVNKDLVLPNFFYYLIANKSFFNDL 358

Query: 343 CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
            K   A GS  + S+K   +    V VP +K Q +I N+++ +T +ID L+E I + I  
Sbjct: 359 LKD--ATGSTFK-SIKINSLIEKKVPVPSLKTQKEIANLLDDKTEKIDNLIENITKQIKK 415

Query: 403 LKERRSSFIAAAVTGQ 418
           L+E R S I  AVTG+
Sbjct: 416 LQEYRKSIIGEAVTGK 431



 Score = 72.8 bits (177), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 108/212 (50%), Gaps = 11/212 (5%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYG-NIIQKLETRNMG 274
           K K SGIEW+G +P +W       +V+E N +N  +  +N LSL     +I   E  ++G
Sbjct: 6   KYKPSGIEWIGDIPKNWNFVSCRLIVSERNERNKGMKNNNYLSLMANIGVIPYEEKGDIG 65

Query: 275 -LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG--IDST 331
             KPE+ E  +IV  G+++   ++       +        GI +  Y+ +  +   I+  
Sbjct: 66  NKKPENLEKCKIVYEGDLIINSMNYFIGSYGISKYD----GICSPVYIVLYANTKVIEPR 121

Query: 332 YLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
           +   +  +     V  + G+G+   R+++ ++ +K + + VP ++EQ +I + ++ +T +
Sbjct: 122 FAFRVFENPKFQGVAQSFGNGILEHRRAINWDILKNIKIPVPLLEEQRNILSFLDKKTEK 181

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           ID L+   E+ I LL+E R S I+  VT  +D
Sbjct: 182 IDALISDKEKLIKLLREYRQSIISETVTKGLD 213


>gi|212690633|ref|ZP_03298761.1| hypothetical protein BACDOR_00120 [Bacteroides dorei DSM 17855]
 gi|212666733|gb|EEB27305.1| hypothetical protein BACDOR_00120 [Bacteroides dorei DSM 17855]
          Length = 423

 Score =  136 bits (342), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 107/435 (24%), Positives = 198/435 (45%), Gaps = 37/435 (8%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRF--------TKLNTGRTSESGKDIIYIGLEDV 56
           K Y  YKDSGV+WIG IP HW+ + I R         T L++     S K + ++   D+
Sbjct: 3   KKYDAYKDSGVKWIGEIPNHWEAIKISRVHPIIGSGTTPLSSREDYYSEKGLNWLQTGDL 62

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
            +G      K    +  D   +  +    ++    G  + K  + D +   +    ++ P
Sbjct: 63  NNGLITETSKKITPKAVDECKMKFYPIHSVVIAMYGATIGKVGLLDIETATNQACCIIVP 122

Query: 117 -KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
            K + P+    +   I   + +     G    +     I  + +P+PPL+EQ  I   + 
Sbjct: 123 SKRICPKYT--FYSFIIAKEELLLSSFGGGQPNISQDIIRKLKVPVPPLSEQQSIASYVD 180

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV- 234
            +T +ID +I +  + IE L E KQ+L++  VT+GLNP+  +KDSG+ W+G +P HW++ 
Sbjct: 181 VKTEKIDKMIAKAEKKIEYLGELKQSLITRAVTRGLNPNTPLKDSGVNWIGNIPMHWDIA 240

Query: 235 --KPFFALVTELNRKNTKLIESNILS-LSYGNII--QKLETRNMGLKPESYETYQIVDPG 289
             + F  L+        +L+ S     L  GN          NM L+P+ Y      D  
Sbjct: 241 CLRFFLRLINGRAYSQNELLPSGKYKVLRVGNFFTNDSWYYSNMELEPDKY-----CDKD 295

Query: 290 EIVFRFID-----LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK 344
           ++++ +       + N+ +++    + +  + TS         +D  Y  +L+R+    K
Sbjct: 296 DLLYAWSASVGPYIWNEAKTIYHYHIWKVQLATS---------MDKMYSYYLLRAVTNQK 346

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           +    GS +   +   D+ +  + +PP+ EQ  I   ++ + ++ID ++   ++ I  L+
Sbjct: 347 MSDMHGSTMMH-ITMGDMNKTKIPIPPLSEQQQIATYLDTKCSKIDHIIATQKKKIAYLQ 405

Query: 405 ERRSSFIAAAVTGQI 419
           E + S I   VTG+I
Sbjct: 406 ELKQSLITNVVTGKI 420


>gi|237725172|ref|ZP_04555653.1| type I restriction-modification system [Bacteroides sp. D4]
 gi|229436438|gb|EEO46515.1| type I restriction-modification system [Bacteroides dorei
           5_1_36/D4]
          Length = 423

 Score =  135 bits (341), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 107/435 (24%), Positives = 198/435 (45%), Gaps = 37/435 (8%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRF--------TKLNTGRTSESGKDIIYIGLEDV 56
           K Y  YKDSGV+WIG IP HW+ + I R         T L++     S K + ++   D+
Sbjct: 3   KKYDAYKDSGVKWIGEIPNHWEAIKISRVHPIIGSGTTPLSSREDYYSEKGLNWLQTGDL 62

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
            +G      K    +  D   +  +    ++    G  + K  + D +   +    ++ P
Sbjct: 63  NNGLITETSKKITPKAVDECKMKFYPIHSVVIAMYGATIGKVGLLDIETATNQACCIIVP 122

Query: 117 -KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
            K + P+    +   I   + +     G    +     I  + +P+PPL+EQ  I   + 
Sbjct: 123 SKRICPKYT--FYSFIIAKEELLLSSFGGGQPNISQDIIRKLKVPVPPLSEQQSIASYLD 180

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV- 234
            +T +ID +I +  + IE L E KQ+L++  VT+GLNP+  +KDSG+ W+G +P HW++ 
Sbjct: 181 VKTEKIDKMIAKAEKKIEYLGELKQSLITRAVTRGLNPNTPLKDSGVNWIGNIPMHWDIA 240

Query: 235 --KPFFALVTELNRKNTKLIESNILS-LSYGNII--QKLETRNMGLKPESYETYQIVDPG 289
             + F  L+        +L+ S     L  GN          NM L+P+ Y      D  
Sbjct: 241 CLRFFLRLINGRAYSQNELLPSGKYKVLRVGNFFTNDSWYYSNMELEPDKY-----CDKD 295

Query: 290 EIVFRFID-----LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK 344
           ++++ +       + N+ +++    + +  + TS         +D  Y  +L+R+    K
Sbjct: 296 DLLYAWSASVGPYIWNEAKTIYHYHIWKVQLATS---------MDKMYSYYLLRAVTNQK 346

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           +    GS +   +   D+ +  + +PP+ EQ  I   ++ + ++ID ++   ++ I  L+
Sbjct: 347 MSDMHGSTMMH-ITMGDMNKTKIPIPPLSEQQQIATYLDTKCSKIDHIIATQKKKIAYLQ 405

Query: 405 ERRSSFIAAAVTGQI 419
           E + S I   VTG+I
Sbjct: 406 ELKQSLITNVVTGKI 420


>gi|52549656|gb|AAU83505.1| restriction endonuclease S subunits [uncultured archaeon
           GZfos29E12]
          Length = 438

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 135/448 (30%), Positives = 215/448 (47%), Gaps = 47/448 (10%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVE-SGTGKY 63
           K YP+YKDS ++WIG IP+ W+V  IK  T    GR       I + GL   E S  G Y
Sbjct: 4   KPYPKYKDSEIEWIGEIPEGWEVNKIKN-TSYVKGR-------IGWHGLTSEEYSDEGAY 55

Query: 64  LP-----KDGNSRQSDTSTVS----------IFAKGQILYGKLGPYLRKAIIADF--DGI 106
           L      KDG     D   V              +  +L  K G   + A+I        
Sbjct: 56  LVTGTDFKDGVIEWEDCHHVGWDRYKEDPYIHLKEDDLLITKDGTIGKVALIKFLPNKAT 115

Query: 107 CSTQFLVLQP--KDVLPELLQGWLLSIDVTQRI-EAICEGATMSHADWKGIGNIPMPIPP 163
            ++   +++P  K   P+ +  W+L+  V +R  + I  GAT+SH   +       PIP 
Sbjct: 116 LNSGIFLVRPLNKKYFPKFMY-WMLNSTVFERFFDYIKTGATISHLYQETFERFFFPIPL 174

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
             EQV I   +  +T +ID LI +  R IELLKEK+ AL+ + VTKGL+P+VKMKD GI 
Sbjct: 175 KQEQVAIASFLDKKTAKIDALIEKDKRLIELLKEKRTALIDHAVTKGLDPNVKMKDFGIV 234

Query: 224 WVGLVPDHWEVKPFFALVTELNR-----KNTKLIESNILSLSYGNIIQKLETRNMGLKPE 278
           W+G +P+  ++ PF   V  +N+     ++ +L E +  S  Y  I + +     G+K  
Sbjct: 235 WIGKIPEDAKIMPF-RRVCYVNQGLQFPEDKRLSEPDEKSKIYITI-KYIHADEDGVK-- 290

Query: 279 SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVM--ERGIITSAYMAVKPHG-IDSTYLAW 335
               Y    P  ++ +  D+    R+  + +V+  + G+  + +  V  +  ID  YL +
Sbjct: 291 ---EYIPNPPRGVICKKEDVLL-ARTGATGEVITNQEGVFHNNFFKVNYNSKIDRDYLVY 346

Query: 336 LMRSYDLCKVFY-AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
            ++   + KV     G      L  +     P ++  I++Q  I   ++ +TA+ID  ++
Sbjct: 347 YLKMDSIKKVLLLKAGVTTIPDLNHDAFLSTPFILYSIEKQKQIAEYLDKKTAKIDKNIK 406

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            IE+ I LL+E + S I   VTG++D+R
Sbjct: 407 LIEKKIKLLEEYKKSLINHVVTGKVDVR 434


>gi|110681177|ref|YP_684184.1| type I restriction-mod [Roseobacter denitrificans OCh 114]
 gi|109457293|gb|ABG33498.1| type I restriction-mod [Roseobacter denitrificans OCh 114]
          Length = 414

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 91/270 (33%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
           ++ Q  I E +  ET RID LI ++ RFI LLKEK+ A++++ VTKG++  V MK SG +
Sbjct: 151 ISTQSKIAEYLDCETARIDGLIEKKTRFIALLKEKRIAVITHAVTKGIDAAVVMKPSGED 210

Query: 224 WVGLVPDHWEVKPFFALVTELN---RKNTKLIESNILSLSYGNI----IQKLETRNMGLK 276
           W+  +P HW V P  AL TE     R+ T+++ +   +  YG I     ++LE R + + 
Sbjct: 211 WLSDIPAHWTVVPPTALFTESKERAREGTQMLSA---TQKYGVIPLAEFERLEQRQVTMA 267

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK--PHGIDSTYLA 334
               +  + V+ G+ V   I +++    L  A+ +  G + S+Y  +K  PH ++  +  
Sbjct: 268 LVHLDKRKHVEVGDFV---ISMRSMDGGLERARAV--GNVRSSYSVLKCGPH-VEGRFYG 321

Query: 335 WLMRSYDLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           +L++S    +      S +R  Q + F   +++ +   P+ EQ  I + I+ +TARID L
Sbjct: 322 YLLKSGLYIQALRLTSSFIRDGQDMNFSHFRKVKLPKLPVAEQAAIADHIDTQTARIDSL 381

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           + K ++SI LL+E+R++ I AAVTG+ID+R
Sbjct: 382 ITKTDRSIALLREKRAALITAAVTGKIDMR 411



 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 63/198 (31%), Positives = 103/198 (52%), Gaps = 15/198 (7%)

Query: 231 HWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP-ESYETYQIVDPG 289
            W+  PF+A+    +  N        + L  G +I   E   +  KP ES E YQ+V+PG
Sbjct: 9   QWKEYPFWAVAKPKSVSNASAESLLSVYLDRG-VIPYSEGGGLVHKPAESLEKYQLVEPG 67

Query: 290 EIVFRFIDLQNDKRSLRSAQVME--RGIITSAYMAVKPHG--IDSTYLAWLMRSYDLC-K 344
           ++V       N++++ R +  +   RGI++ AY   + +G  +D+ +  +L RS     K
Sbjct: 68  DLVL------NNQQAWRGSLGVSTYRGIVSPAYRIFELNGEVVDTRFSHYLFRSRPYVEK 121

Query: 345 VFYAMGS--GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
           +  A  S   +++ +K+  ++ L + VP I  Q  I   ++ ETARID L+EK  + I L
Sbjct: 122 IMLASLSVGDIQRQVKWPLLRVLLLRVPNISTQSKIAEYLDCETARIDGLIEKKTRFIAL 181

Query: 403 LKERRSSFIAAAVTGQID 420
           LKE+R + I  AVT  ID
Sbjct: 182 LKEKRIAVITHAVTKGID 199


>gi|325289015|ref|YP_004265196.1| restriction modification system DNA specificity domain protein
           [Syntrophobotulus glycolicus DSM 8271]
 gi|324964416|gb|ADY55195.1| restriction modification system DNA specificity domain protein
           [Syntrophobotulus glycolicus DSM 8271]
          Length = 443

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 127/466 (27%), Positives = 196/466 (42%), Gaps = 79/466 (16%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPI-----------------KRFTK------LNTGRT 41
           K Y  YKDSG++WIG IP HW+V                      FT       L TG  
Sbjct: 2   KKYNSYKDSGIEWIGEIPGHWEVKKFGYISYMKGRIGWQGLKQAEFTSNPEDPFLITGMN 61

Query: 42  SESGK---DIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKA 98
              GK   D +Y  LE+  +   +   K+ +   +   T+     G++LY    PY  KA
Sbjct: 62  FHDGKIRWDEVYHILEERYNEAPEIQLKESDVLFTKDGTI-----GKLLYVDSIPYPHKA 116

Query: 99  IIADFDGICSTQFLVLQPKDVL--PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN 156
            +       ++  LVL+P +    P  +   L  +     +E    G T      + +G 
Sbjct: 117 SL-------NSHLLVLRPLNNFYNPRFIYYQLKGLPFKHHVELTKTGTTFYGITQEAMGQ 169

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVK 216
               +P L EQ  I   +  +T  ID LI ++ R +EL +E+K A+++  VTKG+NPD  
Sbjct: 170 YKALLPSLPEQTAIANYLDRKTAEIDELIADKKRLLELYEEEKTAIINQAVTKGINPDAP 229

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           MKDSGIEW+G +P+HWEVK              K + + +L    G ++   +     LK
Sbjct: 230 MKDSGIEWLGEIPEHWEVKRL------------KYVANIVL----GKMLTTEDKGEYYLK 273

Query: 277 PE------SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGII----------TSAY 320
           P       ++ +  + D  E+ F   +L   + +     V E G +             Y
Sbjct: 274 PYLRAANLNWLSVNVDDVKEMWFSERELNKYRLNRNDLLVSEGGEVGRTCIWKEELEECY 333

Query: 321 MAVKPHGI------DSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIK 373
           +    H +      DS Y   L   Y     F  + + +    L  E +K +  + PP +
Sbjct: 334 IQNSVHKVTLNDNSDSNYFLQLFYLYGKKGAFDLIVNKISIAHLTVEKLKEIKFITPPFE 393

Query: 374 EQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           EQ  I + I  E A ID    + E+ I  L E R++ I+  VTG+I
Sbjct: 394 EQQSIVHHIKTECASIDAKKFRNEKLIEFLTEYRTALISEVVTGKI 439


>gi|332885123|gb|EGK05375.1| hypothetical protein HMPREF9456_02874 [Dysgonomonas mossii DSM
           22836]
          Length = 452

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 126/462 (27%), Positives = 206/462 (44%), Gaps = 62/462 (13%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K Y  YK S + ++  IP HW+ + ++    L  G T +S  D   IG  ++E+      
Sbjct: 2   KKYDSYKLSHIDFLDHIPSHWQEIRMRFLGYLYGGLTGKSADDFNQIG--NIENKAFIPF 59

Query: 65  PKDGNSRQSDTSTV-----------SIFAKGQIL-------YGKLGPYLRKAIIAD---- 102
               N+ + D S +           +   KG +        Y  +G   + A++ D    
Sbjct: 60  TNIANNSKIDISKLQEVIITDGEKQNKAQKGDLFFLMSSENYEDVG---KSAVLCDDVED 116

Query: 103 --FDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
              +  C   F V+  K++  E L   L S ++   +     G T  +     + ++ + 
Sbjct: 117 MYLNSFCKG-FRVV-AKNINSEFLNYQLSSSEIRHNLLTEANGFTRINLKIDKVNDLIVA 174

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           IP   EQ  I   +  +T  ID LI ++ R IEL +E+K A+++  VTKG++ +VKM+DS
Sbjct: 175 IPTEHEQTAIASFLDRKTAEIDQLIADKKRLIELYEEEKAAIINQAVTKGIDSNVKMQDS 234

Query: 221 GIEWVGLVPDHWEVKPF---FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           GIEW+G +P HWEV+ F   F+    L      L +  I  +SYG I  K    +  + P
Sbjct: 235 GIEWLGEIPGHWEVRRFNSLFSFSRGLTITKENLQDEGIPCISYGEIHSKY---SFEVNP 291

Query: 278 ESYETYQIVDPGEIV-----------FRFIDLQND-KRSLRSAQVMERGIITSAYMAVKP 325
           E  +  + VD   ++           F F D   D K S     +       + Y  +  
Sbjct: 292 EK-DILKCVDKNYLISSEKSLLNHGDFVFADTSEDIKGSGNFTYLNSETRAFAGYHTIIA 350

Query: 326 HGIDS---TYLAWLMRSYDL-----CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFD 377
           + I++    Y+A+   S        CKV       + QS+    +K   +L+PPI EQ  
Sbjct: 351 NPIENFMHRYVAYFFDSLSFRNQIRCKVTGTKVYSITQSI----LKCTFILLPPIHEQNS 406

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           I   I+ E +RI+  +EK ++ I LL E R++ I+  VTG+I
Sbjct: 407 IVQYIDAECSRINSKIEKTKKLIDLLTEYRTTLISEIVTGKI 448


>gi|126664813|ref|ZP_01735797.1| type I restriction-modification [Marinobacter sp. ELB17]
 gi|126631139|gb|EBA01753.1| type I restriction-modification [Marinobacter sp. ELB17]
          Length = 444

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 121/460 (26%), Positives = 200/460 (43%), Gaps = 83/460 (18%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTG--------------------RTSE 43
           +  Y +YKD+ + WI  IP  W++  + +   +  G                     T+ 
Sbjct: 3   FPRYSEYKDTEINWIAQIPTGWQIASLSKLFSIKAGGDVNTDVFSETRTHDRPFPIYTNA 62

Query: 44  SGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF 103
           +  +I+Y       +   KY P          + +++  +G + +     ++  AII   
Sbjct: 63  NNPNIVY-----GYTSKAKYGP----------NCITVSGRGYVGFAAFRDHIFDAII--- 104

Query: 104 DGICSTQFLVLQPKDVLPELLQGWLLS--IDVTQRIEAICEGATMSHADWKGIGNIPMPI 161
                 + LVL PK  L      + ++  +D  +   AI + +T   A +K      +  
Sbjct: 105 ------RLLVLTPKKDLNCKFFEYFINEVVDFREESSAIGQLSTNQIAPYK------VAF 152

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           P   EQ  I   +  ET +IDTLI E+ R IELLKEK+QA++S+ VTKGL+PDV +KDSG
Sbjct: 153 PDCREQSKITHFLDHETAKIDTLIHEQKRLIELLKEKRQAVISHAVTKGLDPDVPIKDSG 212

Query: 222 IEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE 281
           +EW+G VP HW V         +    T  +E     ++ G              P  + 
Sbjct: 213 VEWLGDVPAHWGVATIRRFAKAVRTGGTPSLEMPNSEIADG---------INWFTPGDFN 263

Query: 282 TYQIVDPGEIVFRFIDLQN-DKRSLRSAQVMERGI---------ITSAYMA-------VK 324
              ++   E   R   + + D +      V+  GI         +   + A       V 
Sbjct: 264 GSLMLHESEKQLRISSISSGDAKLFPGGSVLVVGIGATLGKVAKVDDDFSANQQINVIVP 323

Query: 325 PHGIDSTYLAWLMRSYDLCKVFYAMGS--GLRQSLKFEDVKRLPVLVPPIKEQFDITNVI 382
              I+  +L + + +      F +  S  G+    K +D+    +++PP++EQ  IT  +
Sbjct: 324 GKRINGHFLVYSLSAQKSQMRFVSNASTIGIMNQEKTKDIV---LVLPPVEEQTQITESL 380

Query: 383 NVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           +     +D LV K    I+LLKERRS+ I+AAVTG+ID+R
Sbjct: 381 DRGVQNLDQLVIKAASGILLLKERRSALISAAVTGKIDVR 420


>gi|265754307|ref|ZP_06089496.1| predicted protein [Bacteroides sp. 3_1_33FAA]
 gi|263235016|gb|EEZ20571.1| predicted protein [Bacteroides sp. 3_1_33FAA]
          Length = 423

 Score =  134 bits (337), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 106/435 (24%), Positives = 197/435 (45%), Gaps = 37/435 (8%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRF--------TKLNTGRTSESGKDIIYIGLEDV 56
           K Y  YKDSGV+WIG IP HW+ + I R         T L++     S K + ++   D+
Sbjct: 3   KKYDAYKDSGVKWIGEIPNHWEAIKISRVHPIIGSGTTPLSSREDYYSEKGLNWLQTGDL 62

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
            +G      K    +  D   +  +    ++    G  + K  + D +   +    ++ P
Sbjct: 63  NNGLITETSKKITPKAVDECKMKFYPIHSVVIAMYGATIGKVGLLDIETATNQACCIIVP 122

Query: 117 -KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
            K + P+    +   I   + +     G    +     I  + +P+PPL+EQ  I   + 
Sbjct: 123 SKRICPKYT--FYSFIIAKEELLLSSFGGGQPNISQDIIRKLKVPVPPLSEQQSIASYLD 180

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV- 234
            +T +ID +I +  +  E L E KQ+L++  VT+GLNP+  +KDSG+ W+G +P HW++ 
Sbjct: 181 VKTEKIDKMIAKAEKKTEYLDELKQSLITRAVTRGLNPNTPLKDSGVNWIGNIPMHWDIA 240

Query: 235 --KPFFALVTELNRKNTKLIESNILS-LSYGNII--QKLETRNMGLKPESYETYQIVDPG 289
             + F  L+        +L+ S     L  GN          NM L+P+ Y      D  
Sbjct: 241 CLRFFLRLINGRAYSQNELLPSGKYKVLRVGNFFTNDSWYYSNMELEPDKY-----CDKD 295

Query: 290 EIVFRFID-----LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK 344
           ++++ +       + N+ +++    + +  + TS         +D  Y  +L+R+    K
Sbjct: 296 DLLYAWSASVGPYIWNEAKTIYHYHIWKVQLATS---------MDKMYSYYLLRAVTNQK 346

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           +    GS +   +   D+ +  + +PP+ EQ  I   ++ + ++ID ++   ++ I  L+
Sbjct: 347 MSDMHGSTMMH-ITMGDMNKTKIPIPPLSEQQQIATYLDTKCSKIDHIIATQKKKIAYLQ 405

Query: 405 ERRSSFIAAAVTGQI 419
           E + S I   VTG+I
Sbjct: 406 ELKQSLITNVVTGKI 420


>gi|296116346|ref|ZP_06834962.1| type I restriction-modification system specificity subunit
           [Gluconacetobacter hansenii ATCC 23769]
 gi|295977165|gb|EFG83927.1| type I restriction-modification system specificity subunit
           [Gluconacetobacter hansenii ATCC 23769]
          Length = 322

 Score =  133 bits (335), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 99/335 (29%), Positives = 170/335 (50%), Gaps = 54/335 (16%)

Query: 127 WLLSIDVTQ-RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
           W+L  ++ +  I+    G+T++H       N   P+P   EQ  I   +  E  +ID LI
Sbjct: 3   WVLESNIFKIFIDLHSHGSTINHLYQNVFENFSFPLPAFPEQQAIASFLDRECGKIDALI 62

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK---------- 235
            E+ R I LL EK+QA++S+ VTKGLNP+  MKDSGI W+G+VP+ WEV           
Sbjct: 63  AEQERLIALLAEKRQAVISHAVTKGLNPNAPMKDSGIPWIGMVPEGWEVSRLKYLVQCYD 122

Query: 236 -----PFFALVTELNRKNTKLI---ESNILSLSYGNIIQKLETRNMGLKPESYETYQ--- 284
                PF  ++ ++N + T      + N +S  +G          +G +  S + Y    
Sbjct: 123 GIQMGPFGGMLLDINSEPTGYKVYGQENTISGDFG----------LGHRWISTDRYNDLR 172

Query: 285 --IVDPGEIVFRFIDLQNDKRSLRSAQVMER----GIITSAYMAVKPHGIDST-----YL 333
              ++ G++V         K SL +A+++ +    GI  S  + ++   +D +     +L
Sbjct: 173 RYSLNGGDLVL------TRKGSLGNARLVSKLPYPGIADSDTIRIR---VDKSKVYPEFL 223

Query: 334 AWLMR--SYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
           A L+   +Y   ++  +    +   L  +++  L V+ PPI EQ +I N + + +   D 
Sbjct: 224 ATLLHEANYIESQINASKRGAILSGLNTKNISDLIVIYPPIYEQNNILNYLKISSEEFDC 283

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
            +++   +I LLKERR++ I+AAVTG+ID+R +S+
Sbjct: 284 SIQQSAIAITLLKERRAALISAAVTGKIDVRAQSK 318


>gi|237709675|ref|ZP_04540156.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|229456311|gb|EEO62032.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
          Length = 428

 Score =  133 bits (334), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 118/433 (27%), Positives = 204/433 (47%), Gaps = 23/433 (5%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESG--KDIIYIGLEDVESGTGK 62
           K Y  YKDSGV+WIG IP HW+VVP+KR      G T      +D  YI L        K
Sbjct: 2   KKYDAYKDSGVKWIGEIPNHWEVVPLKRTGSFENGLTYSPNDIRDKGYIVLRSSNIQNSK 61

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
              +D    +S  + + +     I+  + G        A FDG  +  F     +   P 
Sbjct: 62  MNYEDTVYVESVPNDLLVKKGDIIICSRNGSASLVGKCAKFDGKIAATFGAFMMR-YSPS 120

Query: 123 LLQGW-LLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
           +   +   S  +  R  + +   +T++      I  +  P+PPL+EQ  I   + A+T +
Sbjct: 121 INNEYAFFSFQILMRNYKGLFTTSTINQLTKNVIAQMVCPLPPLSEQQAIASYLDAKTEK 180

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           ID +I +  + IE L E KQ+L++  VT+GLNP+  +KDSG++W+G VP+HWE      +
Sbjct: 181 IDKMIAKAEKKIEYLGELKQSLITRAVTRGLNPNASLKDSGVKWIGKVPEHWETIKLSRV 240

Query: 241 VTELNRKNTKL-IESNILSLSYGNIIQKLETRNMGLKPESYE--TYQIVDPGEIVFRFID 297
            + +    T L  + +  S    N +Q  +  N GL  ++ +  T + +D  E   +F  
Sbjct: 241 YSYIGSGTTPLSSQEDYYSEEGYNWLQTGDLNN-GLITQTSKKITKKAID--ECRMKFYP 297

Query: 298 LQNDKRSLRSAQVMERGII------TSAYMAVKPHGIDS---TYLAWLMRSYDLCKVFYA 348
             +   ++  A + + G++        A   + P    +   T+ +++    +L  +  +
Sbjct: 298 KHSVVIAMYGATIGKVGLLDLESTTNQACCVISPTQKMNPLFTFYSFMAAKKEL--LLAS 355

Query: 349 MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRS 408
            G G + ++  + +K+L V VPP++EQ  I   +  E   ID ++   ++ I  L+E + 
Sbjct: 356 FGGG-QPNISQDIIKKLRVPVPPLEEQNAIILSLKKECDTIDHIIATQKKKIAYLQELKQ 414

Query: 409 SFIAAAVTGQIDL 421
           S I   VTG+I +
Sbjct: 415 SLITNVVTGKIKV 427


>gi|238920394|ref|YP_002933909.1| restriction modification system DNA specificity domain protein
           [Edwardsiella ictaluri 93-146]
 gi|238869963|gb|ACR69674.1| restriction modification system DNA specificity domain protein
           [Edwardsiella ictaluri 93-146]
          Length = 435

 Score =  132 bits (333), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 118/437 (27%), Positives = 197/437 (45%), Gaps = 33/437 (7%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT----------SESGKDIIYIGLEDV 56
           Y  YK+SGV+WI  +P+ W +V IK +  +  G +          SE      YI  +D+
Sbjct: 9   YDTYKNSGVEWIEQVPEGWGLVKIKNYADVFNGDSLNDKQKAKYESEDQSHRSYISSKDI 68

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV--L 114
           +    K   ++G  R    S+  +      L    G    K I      +C    L   L
Sbjct: 69  DVNYSKINYQNG-LRIPKGSSYKVCPSNSTLMCIEGGSAGKKIAYTNQEVCFVNKLACFL 127

Query: 115 QPKDVLPELLQGWLLSIDVTQR----IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
             K +    L  +L S+    +    +  +  G ++S      I N  + +P   EQV I
Sbjct: 128 ASKRIDSHFLYYYLSSVTFKSQFFNSMTGLIGGVSIS-----AIKNFWLVLPSPTEQVAI 182

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              +  +  +ID  IT + + I LLKE+KQ L+    T+GL+P V MKDSG++W+G +P+
Sbjct: 183 ASFLSKKLSQIDEAITTKEQQISLLKERKQILIQQAATQGLDPCVPMKDSGVDWIGKIPE 242

Query: 231 HWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE-TYQIVDPG 289
           HW+V  F  L ++ +R   +  +  + S   G +  +   R  G      E  YQ +  G
Sbjct: 243 HWQVIRFKNLFSQ-SRIPVRKEDGVVTSYRDGQVTLRSNRRLDGYTEAIIEGGYQGIRKG 301

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST--YLAWLMRSYDLCKVFY 347
           ++V   +D       +  +     G  T  Y+   P   D +  Y A+L+R   L K   
Sbjct: 302 QLVLNSMDAFEGAIGVSESD----GKCTPEYVICDPVRADVSQYYFAYLLREMALAKYIQ 357

Query: 348 AMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            + + +RQ    ++F ++    +++PP  EQ  I   I  E  +I+  VE ++  I  LK
Sbjct: 358 VICNAVRQRAVRIRFNNLASRFMVLPPSDEQEKIVEFIESEKGKINKGVEHLKGQIEKLK 417

Query: 405 ERRSSFIAAAVTGQIDL 421
           E +++ I +AVTG+I +
Sbjct: 418 EYKTTLINSAVTGKIKV 434


>gi|311694470|gb|ADP97343.1| type I site-specific restriction-modification system, S subunit
           [marine bacterium HP15]
          Length = 427

 Score =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 119/437 (27%), Positives = 199/437 (45%), Gaps = 48/437 (10%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLP- 65
           Y  YKDSG  W+G IP +W     K   ++  G+     K I+     +  SG   YL  
Sbjct: 10  YEAYKDSGADWLGMIPINWTSKKFKYLARVKKGKVP---KRIV----SENRSGLPPYLSM 62

Query: 66  -----KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
                 + N    D   + + + G IL               +DG  + +F+V +   V 
Sbjct: 63  EYLRGAEANQFVEDRDAI-VVSDGSILL-------------LWDGSNAGEFVVGRGGVVS 108

Query: 121 PELLQGWLLSID---------VTQ-RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
             L      S+D         VT+  + +   G  + H D + + N  + IP L EQ LI
Sbjct: 109 STLAAIDFFSVDRKFAWYACQVTEIELRSTTVGMGIPHVDGEQLKNSFLAIPSLDEQSLI 168

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
            + +  +T +ID  I  + + I LLKE+KQ ++   VT+GL+P V MK SG++W+G +P 
Sbjct: 169 AKFLDKKTTQIDEAIAIKEQQIVLLKERKQIIIQKAVTQGLDPTVPMKLSGVDWIGEIPK 228

Query: 231 HWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE-TYQIVDPG 289
           HWEV  F  L ++ +R   ++ +  + S   G +  +   R  G      E  YQ +  G
Sbjct: 229 HWEVVRFKNLFSQ-SRLPVRIGDGVVTSYRDGQVTLRTNRRLEGYTEAIIEGGYQGIRKG 287

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH--GIDSTYLAWLMRSYDLCKVFY 347
           ++V   +D       +  +     G  T  Y+   P+  GI   Y A+L+R   L K   
Sbjct: 288 QLVLNSMDAFEGAIGVSDSD----GKCTPEYVICDPNRGGISQYYFAYLLREMALGKYIQ 343

Query: 348 AMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            + + +RQ    +++ ++    ++VPP  EQ +I   I  E  +I   ++ ++  I  LK
Sbjct: 344 VICNAVRQRAVRIRYNNLAPRFMVVPPESEQEEIVKFIESEKVKIGDGIDHLQSQIEKLK 403

Query: 405 ERRSSFIAAAVTGQIDL 421
           E +++ I +AVTG+I +
Sbjct: 404 EYKTTLINSAVTGKIKI 420


>gi|171915570|ref|ZP_02931040.1| putative restriction endonuclease S subunit [Verrucomicrobium
           spinosum DSM 4136]
          Length = 299

 Score =  132 bits (332), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 90/284 (31%), Positives = 153/284 (53%), Gaps = 14/284 (4%)

Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQAL 202
           G TM +   + +  +P+  P    Q  I   +  ET RID L++ + R +EL+ EK++AL
Sbjct: 16  GTTMDNLGAETVAELPIQAPSPPRQHSIATYLDRETKRIDELVSVKERLLELVAEKRRAL 75

Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYG 262
           ++  VT+GLNP   ++DSGI W+G +P+HW+V+    L TE + +++   E  +L++S+ 
Sbjct: 76  ITRAVTRGLNPKAALRDSGIPWLGAIPEHWQVERSKWLFTERDERSST-GEEEMLTVSHL 134

Query: 263 NIIQKLETRNMGL-KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER--GIITSA 319
             +     +++ + + E+ E Y++  P ++V       N   +   A    R  G+++ A
Sbjct: 135 TGVTPRAEKDVNMFEAETTEGYKLCQPNDLVI------NTLWAWMGAMGTARAPGMVSPA 188

Query: 320 YMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQ 375
           Y    P   +DS Y+  L+R     +       G+   R  L  E +  +   VPP++EQ
Sbjct: 189 YHVYTPGDRLDSDYVDALVRIPIFAQEAIRFSKGVWSSRLRLYPEGLYEIWFPVPPLEEQ 248

Query: 376 FDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
             I   I  ETA++D L    E++I LLKERR++ I+AAVTG+I
Sbjct: 249 RAIVTHIARETAKLDALRASAERTIALLKERRAALISAAVTGKI 292



 Score = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 91/208 (43%), Gaps = 19/208 (9%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           +DSG+ W+GAIP+HW+V   K        R+S   ++++ +      +G      KD N 
Sbjct: 91  RDSGIPWLGAIPEHWQVERSKWLFTERDERSSTGEEEMLTVSH---LTGVTPRAEKDVNM 147

Query: 71  RQSDTST-VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLL 129
            +++T+    +     ++   L  ++     A   G+ S  + V  P D L         
Sbjct: 148 FEAETTEGYKLCQPNDLVINTLWAWMGAMGTARAPGMVSPAYHVYTPGDRLDSDY----- 202

Query: 130 SIDVTQRIEAICEGA-TMSHADW--------KGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            +D   RI    + A   S   W        +G+  I  P+PPL EQ  I   I  ET +
Sbjct: 203 -VDALVRIPIFAQEAIRFSKGVWSSRLRLYPEGLYEIWFPVPPLEEQRAIVTHIARETAK 261

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVT 208
           +D L     R I LLKE++ AL+S  VT
Sbjct: 262 LDALRASAERTIALLKERRAALISAAVT 289


>gi|194288966|ref|YP_002004873.1| type I restriction-modification methylase s subunit [Cupriavidus
           taiwanensis LMG 19424]
 gi|193222801|emb|CAQ68804.1| type I restriction-modification methylase S subunit [Cupriavidus
           taiwanensis LMG 19424]
          Length = 458

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 116/452 (25%), Positives = 208/452 (46%), Gaps = 44/452 (9%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD----IIYIGLEDVESGTGK 62
           Y  Y+DSG+ W+G +P HW+V  ++   + N  ++  S  D    + ++ ++ +      
Sbjct: 6   YAAYRDSGIDWLGDMPAHWQVRRLRFAAEFNPSKSEVSHLDRDTLVSFLPMDAIGEEGSL 65

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGIC------STQFLVLQP 116
            L +     Q +T   + F +G + + K+ P       A   G+       +T+ +V +P
Sbjct: 66  VLEQVRQVSQVETG-YTYFHEGDVAFAKITPCFENGKGAVMRGLLGGVGFGTTELIVARP 124

Query: 117 K-DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIG-----NIPMPIPPLAEQVLI 170
           + DV       WL     +     + EGA       K +      +  +  PPL+EQ  I
Sbjct: 125 RSDVTCSEYLHWLF---CSIPFRKLGEGAMYGAGGQKRVPEDFARDFAIAFPPLSEQNAI 181

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              + +ET +IDTLI+E+ + + LL EK+QA +S IVT+GL P V++K  G +W+G +P 
Sbjct: 182 VTFLYSETSKIDTLISEQDKLLVLLAEKRQATISRIVTRGLEPKVQIKSVGADWLGEIPI 241

Query: 231 HWEVKPFFALVTELNRKNTKLIES---------NILSLSY--GNIIQKLETRNMGLKPES 279
           HW+ K    L + + +  +   E+          +L +    G +    E + +  + E 
Sbjct: 242 HWQAKRVKWLTSSIEQGWSPQCENYPAEGENEWGVLKVGCVNGGVFDAAENKKLPPELEP 301

Query: 280 YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVM----ERGIITSAYMAVKPHGIDST--YL 333
           +  Y +   G+++   I   N +  + SA V+     R ++      ++      T  +L
Sbjct: 302 FPEYSL-RKGDLL---ISRANTRELVGSAAVVPKDFHRLLLCDKLYRLRLDQAKCTPEFL 357

Query: 334 AWLMRSYDLCKVFYAMGSGLRQSL---KFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
           A  + + +         +G   S+       +  L V +PP +EQ  I + +N E  R++
Sbjct: 358 AAYLATGEARGQIELGATGASSSMLNIGQSVIMDLLVPLPPAEEQAAIMDFLNAELDRLE 417

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            L     +SI LLK RR++ I AAVTG+ID+R
Sbjct: 418 RLSLAANKSIDLLKARRTALITAAVTGKIDVR 449


>gi|332666806|ref|YP_004449594.1| restriction modification system DNA specificity domain-containing
           protein [Haliscomenobacter hydrossis DSM 1100]
 gi|332335620|gb|AEE52721.1| restriction modification system DNA specificity domain protein
           [Haliscomenobacter hydrossis DSM 1100]
          Length = 428

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 128/458 (27%), Positives = 207/458 (45%), Gaps = 62/458 (13%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRF-------TKLNTGRTSESGKDIIYIGL 53
           M + + YP YK+SGV+WI  +P HW+VV +KR        T ++    S S   ++Y   
Sbjct: 1   MMNVQKYPAYKNSGVEWIETVPSHWEVVKLKRLFCEKKKITNVDLPCGSISFGKVVYKDE 60

Query: 54  EDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGP-----YLRKAIIADFDGICS 108
           E +   T K              +    +KG+ L   L        LR A+ +D D + S
Sbjct: 61  EKIPEATKK--------------SYQAVSKGEYLLNPLNLNYDLISLRIAL-SDKDVVVS 105

Query: 109 TQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
           + ++VL     L +    WLL       ++ +  G   +  ++  IG+  +  PPL EQ 
Sbjct: 106 SGYIVLNSIVKLDKTYFKWLLHRYDVAFMKTLGSGVRQT-INFSDIGDSELIFPPLPEQT 164

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I + +  +T  ID  I  + + IELLKE++Q L+   VT+GLNP+VKMK SG+EW+G V
Sbjct: 165 AIAQFLDRKTALIDQAIDIKQKQIELLKERRQILIHQAVTRGLNPEVKMKASGVEWIGEV 224

Query: 229 PDHWEV-------KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE 281
           P+ WEV       K  + L      K   L      ++  G I++K              
Sbjct: 225 PEGWEVVRLKTLGKIKYGLGQPPKTKEDGLPLIRATNVERGRIVEK-------------- 270

Query: 282 TYQIVDPGEIVFRFIDL--QNDKRSLRS-AQVMERGIITSAY--------MAVKPHGIDS 330
               VDP +I +    +  +ND   +RS A   +  II   Y        M + P  I+ 
Sbjct: 271 DLIFVDPEDIPWERDPMLKENDIIVVRSGAYTGDSAIIPKHYAGSIAGYDMVLTPTSINP 330

Query: 331 TYLAW-LMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
            +L++ L+  Y L    Y +     Q  L  E++ +  ++ PP  EQ  I   +   + +
Sbjct: 331 RFLSYTLLAKYVLYDQLYLLRMRAAQPHLNAEELGQTIIVCPPKLEQQQIFEYLENISKK 390

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
           I   +   +Q I  L+E +++ I +AVTG+I +   +Q
Sbjct: 391 IATAITLKQQEIAKLQEYKATLINSAVTGKIKVGSHAQ 428


>gi|237809016|ref|YP_002893456.1| restriction modification system DNA specificity domain-containing
           protein [Tolumonas auensis DSM 9187]
 gi|237501277|gb|ACQ93870.1| restriction modification system DNA specificity domain protein
           [Tolumonas auensis DSM 9187]
          Length = 421

 Score =  131 bits (330), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 124/441 (28%), Positives = 198/441 (44%), Gaps = 60/441 (13%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y  YKDSGV W+G IP+ W    +K   ++  GR     +      L+D     G Y P 
Sbjct: 10  YEAYKDSGVDWLGEIPEEWSTRKVKYLFRIGRGRVISQQE------LDD----NGCY-PV 58

Query: 67  DGNSRQSD-----TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP---KD 118
             +  Q+D      ST   F   QI +   G       +      C+     LQP   + 
Sbjct: 59  YSSQTQNDGILGYISTFD-FDCEQITWTTDGANAGTVFLRKGKHNCTNVCGTLQPINKQK 117

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           +  E L+   LSI           GA + + +   +  I +  PPL  Q  I   +  +T
Sbjct: 118 ISLEFLKN-ALSIAAQFYKRPDTNGAKIMNGE---MAEIFVTFPPLEAQTAIANFLDEKT 173

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID  I  + + IELLKE+KQ ++   VT+GL+P V MKDSG+EW+G +P HWEV    
Sbjct: 174 AKIDEAIAIKEKQIELLKERKQIIIQQAVTQGLDPTVPMKDSGVEWIGKIPAHWEV---- 229

Query: 239 ALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDL 298
                   + ++ +       +  N +Q   T+  G+ P+  E Y+ +   ++V   I  
Sbjct: 230 --------RRSRFVFCQRKERARSNDVQLSATQAYGVIPQ--EQYEEMVGRKVV--KISF 277

Query: 299 QNDKR----------SLRSAQ-VMER----GIITSAYMAVKP---HGIDSTYLAWLMRSY 340
             DKR          S+RS Q  +ER    G I S+Y+ ++P     ID+ + ++L++  
Sbjct: 278 HLDKRKHVEINDFVISMRSFQGGLERAWASGCIRSSYVVLRPVNSEEIDAGFFSYLLKLP 337

Query: 341 DLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
                     S +R  Q L F++  ++ + +PPI EQ  I + I  +   I+   E    
Sbjct: 338 SYINALQMTASFIRDGQDLNFDNFSQVDLFIPPIDEQRAIFSAIQSKVDEINKATEIFIG 397

Query: 399 SIVLLKERRSSFIAAAVTGQI 419
            I   +E +++ I +AVTG+I
Sbjct: 398 QITKYQEYKTTLINSAVTGKI 418



 Score = 47.4 bits (111), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 84/210 (40%), Gaps = 23/210 (10%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           KDSG++W+G +P+ W  +    L                  +  G +I + E  + G  P
Sbjct: 14  KDSGVDWLGEIPEEWSTRKVKYL----------------FRIGRGRVISQQELDDNGCYP 57

Query: 278 -ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV----MERGI--ITSAYMAVKPHGIDS 330
             S +T      G I     D +    +   A      + +G    T+    ++P     
Sbjct: 58  VYSSQTQNDGILGYISTFDFDCEQITWTTDGANAGTVFLRKGKHNCTNVCGTLQPINKQK 117

Query: 331 TYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
             L +L  +  +   FY         +   ++  + V  PP++ Q  I N ++ +TA+ID
Sbjct: 118 ISLEFLKNALSIAAQFYKRPDTNGAKIMNGEMAEIFVTFPPLEAQTAIANFLDEKTAKID 177

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
             +   E+ I LLKER+   I  AVT  +D
Sbjct: 178 EAIAIKEKQIELLKERKQIIIQQAVTQGLD 207


>gi|148827247|ref|YP_001292000.1| type I restriction modification DNA specificity domain-containing
           protein [Haemophilus influenzae PittGG]
 gi|148718489|gb|ABQ99616.1| type I restriction modification DNA specificity domain protein
           [Haemophilus influenzae PittGG]
          Length = 424

 Score =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 118/440 (26%), Positives = 212/440 (48%), Gaps = 46/440 (10%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTG----RTSESGKDIIYIGLE-----D 55
           + Y  YKDSGV+W+G +P HW ++P K   KL       R+SE   D++ + L+     D
Sbjct: 2   RRYESYKDSGVEWLGEVPSHWNLIPNKYIFKLRKNVVGKRSSEY--DLLSLSLKGVIKRD 59

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           +E+  GK+ P + ++ Q       IF    +   +  P  R   ++ + G+ +  + + +
Sbjct: 60  MENPEGKF-PAEFDTYQEVKEGDFIFCLFDV---EETP--RTVGLSSYHGMITGAYTIFE 113

Query: 116 PKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
             +V  + +  + L++D  +R++ + +G   T+S   +         IPPL+EQ  I + 
Sbjct: 114 TNNVDKKFIYYFYLNLDSDKRLKPLYKGLRNTISKETFFSFNTF---IPPLSEQQKIAQF 170

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HWE
Sbjct: 171 LDDKTAKIDQAVDLAEKQIALLKEHKQILIQNSVTRGLNPDVPLKDSGVEWIGQVPEHWE 230

Query: 234 VKPFFALVTELNR-------KNTKLIESN-------ILSLSYGNIIQKLETRNMGLKPES 279
           +     L +++ R        N K  +++       I  ++  N+     T+ +    +S
Sbjct: 231 ILSIKRL-SQVKRGASPRPIDNPKYFDNDGEYAWVRISDVTASNMYLLETTQKLSNLGKS 289

Query: 280 YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRS 339
           Y    +  PG + F  I     K  +   +V     I   ++    +  ++ +L ++  S
Sbjct: 290 YSVPLM--PGSL-FLSIAGSVGKPIITKIKV----CIHDGFVYFPENKQNTKFLYYIFYS 342

Query: 340 YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
                    MG+ L  +L  + V  + + +PP+ EQ  I + ++ +TA+ID  +      
Sbjct: 343 EQPYIGLGKMGTQL--NLNTDTVGAIKIPIPPLCEQQKIADYLDTQTAKIDQAIALKTAH 400

Query: 400 IVLLKERRSSFIAAAVTGQI 419
           I  LKE +S  I   VTG++
Sbjct: 401 IEKLKEYKSVLINDVVTGKV 420


>gi|259502615|ref|ZP_05745517.1| conserved hypothetical protein [Lactobacillus antri DSM 16041]
 gi|259169430|gb|EEW53925.1| conserved hypothetical protein [Lactobacillus antri DSM 16041]
          Length = 422

 Score =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 72/209 (34%), Positives = 121/209 (57%), Gaps = 9/209 (4%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           KDSGI+WVG +PD+W+  P + +  E+ +KN  + +   L  +YG I++K   +N  ++ 
Sbjct: 7   KDSGIKWVGEIPDNWDSVPIYYVSQEVRKKNNNISQKVALKFTYGTIVRK---KNFSIEE 63

Query: 278 ES-----YETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDST 331
           +S      E Y++V P +IV   ++L  D  + R   V   G ITSAY+ ++  + I+  
Sbjct: 64  DSSLRKTIENYKVVKPKDIVINGLNLNFDFVTQRVGFVTFPGAITSAYIVIRAKNNINEK 123

Query: 332 YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
           YL +L++SYD  K F+ MG G+R+ L F  + ++ +  PP+KEQ  IT+ ++ +  +ID 
Sbjct: 124 YLLYLLKSYDSVKAFHNMGGGVRKILNFSILSKIKIPFPPMKEQKRITDFLDKKCGKIDK 183

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           L+ +I   I  LK+ + S I   VT  +D
Sbjct: 184 LLSQINDEIDTLKKYQHSLIIRVVTKGLD 212



 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 104/417 (24%), Positives = 195/417 (46%), Gaps = 16/417 (3%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGN 69
           KDSG++W+G IP +W  VPI   ++ +     + S K  +      +       + +D +
Sbjct: 7   KDSGIKWVGEIPDNWDSVPIYYVSQEVRKKNNNISQKVALKFTYGTIVRKKNFSIEEDSS 66

Query: 70  SRQSDTSTVSIFAKGQILYG---KLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
            R++  +   +  K  ++ G         ++     F G  ++ ++V++ K+ + E    
Sbjct: 67  LRKTIENYKVVKPKDIVINGLNLNFDFVTQRVGFVTFPGAITSAYIVIRAKNNINEKYLL 126

Query: 127 WLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
           +LL S D  +    +  G      ++  +  I +P PP+ EQ  I + +  +  +ID L+
Sbjct: 127 YLLKSYDSVKAFHNMG-GGVRKILNFSILSKIKIPFPPMKEQKRITDFLDKKCGKIDKLL 185

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN 245
           ++    I+ LK+ + +L+  +VTKGL+ +V  KDSGIEW+G +P+ W V     ++T L+
Sbjct: 186 SQINDEIDTLKKYQHSLIIRVVTKGLDSNVPTKDSGIEWIGTMPEKWNVVKGKFILTLLD 245

Query: 246 RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET-YQIVDPGEIVFRFIDLQNDKRS 304
           R  TK  +  I     G +  + + R  G    + E  YQ VD G++V   +D       
Sbjct: 246 RP-TKKDDEVITCFRDGQVTLRKKRRTDGFTISTKEIGYQGVDVGDLVVHAMDGFAGAIG 304

Query: 305 LRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLR---QSLKFED 361
           +  +    RG   S  + V     +  YL + +R      VF A+  G+R      ++  
Sbjct: 305 ISDS----RG-KASPVLNVMDSSENKNYLKYYLRCCAYLGVFNALAKGIRVRTADTRWST 359

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           +  L   +P   EQ DI++ ++ + A I  L+ +  + + LL + ++S I   VTG+
Sbjct: 360 LANLKFPLPTKNEQKDISDYLDQKCAEIRALINEKNRQLDLLTKYKNSLIFEYVTGK 416


>gi|307826306|ref|ZP_07656513.1| restriction modification system DNA specificity domain protein
           [Methylobacter tundripaludum SV96]
 gi|307732662|gb|EFO03532.1| restriction modification system DNA specificity domain protein
           [Methylobacter tundripaludum SV96]
          Length = 435

 Score =  130 bits (327), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 119/445 (26%), Positives = 206/445 (46%), Gaps = 51/445 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGR---TSESGK---DIIYIGLEDVESGT 60
           Y  YKDSGV+W+G IP+HW++  +K     ++G      E GK   ++ +  + D+  G 
Sbjct: 11  YEIYKDSGVEWLGEIPEHWEIKRLKFIIAEHSGNGFPVEEQGKHTGELPFYKVSDI-GGD 69

Query: 61  GKYLPKDGNSRQSDTSTV---SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
             Y+    N     T+     ++   G ++  K+G  LRK    +   I ++  ++    
Sbjct: 70  SMYISHASNYVNFKTAKKLKWNLIPSGSLITAKIGEALRK----NHRKISTSSSIIDNNC 125

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADW-KGIGNIP-----------MPIPPLA 165
                +  G + +  + + I+           DW    G +P           +P+P   
Sbjct: 126 IAFEAVSIGVVFNYYLHKVIDF----------DWFTNPGAVPCISVPKYKSFHIPLPAFT 175

Query: 166 EQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           EQ  I   +  +T ++D  +  + + I L KE KQ L+   VT+ LNPD  M+DSG+EW+
Sbjct: 176 EQTAIAAFLDRKTAQLDQAVAIKEKQITLFKEHKQILIQNAVTRSLNPDAPMRDSGVEWL 235

Query: 226 GLVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET 282
           G +P HW +   +  F    E       L+  +I +      I + E     +K E    
Sbjct: 236 GKIPAHWAILANRVIFRERVEPGEDGLPLLSVSIHTAVSSEEISEDENIRGRIKIEDKTK 295

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSA--QVMERGIITSAYMAVKPH-GIDSTYLAWLMRS 339
           Y +V  G+I F      N  R+ + A   V  +G+++ AY+   P+  I S+Y  +  R 
Sbjct: 296 YSLVQIGDIAF------NMMRAWQGAIGAVKIKGMVSPAYIVAVPNEKIVSSYFEYQYRC 349

Query: 340 YDLCKVF--YAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
            +  +    Y+ G +  R+ L + + K+L  +VPP++EQ  I   I  E+A+ID  +   
Sbjct: 350 PEFIQQMDRYSKGITDFRKRLYWNEFKQLVTVVPPVEEQTAIVTHIETESAKIDQAISIQ 409

Query: 397 EQSIVLLKERRSSFIAAAVTGQIDL 421
           +Q I  LKE +++ I +AVTG+I +
Sbjct: 410 QQQIDKLKEYKATLINSAVTGKIKV 434


>gi|229520259|ref|ZP_04409685.1| type I restriction-modification system specificity subunit S
           [Vibrio cholerae TM 11079-80]
 gi|167832523|gb|ACA01833.1| type I site-specific restriction-modification system S subunit
           [Vibrio cholerae]
 gi|229342625|gb|EEO07617.1| type I restriction-modification system specificity subunit S
           [Vibrio cholerae TM 11079-80]
          Length = 458

 Score =  130 bits (327), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 108/439 (24%), Positives = 200/439 (45%), Gaps = 24/439 (5%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-SESGKDI---------IY 50
           +K    Y  YK+SG++W+  +P+ W+   +K    + TG + S + KD           Y
Sbjct: 22  IKQMPKYESYKESGIEWLDEVPQTWQTSKLKYLASIFTGDSISPTLKDTYVSTELSGRAY 81

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGIC-ST 109
           I  +D++  T +   ++G     D     +  +   L    G    K I      +C   
Sbjct: 82  IASKDIDVQTSRIDYENGVRIPFDRRHFKVAPEQSTLLCIEGGSAGKKIAYTAQDVCFVN 141

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
           +   +  + VL + L   L S     + +    G  +       I N  + +PP  EQ+ 
Sbjct: 142 KLACIASEKVLNKYLYYSLFSEPFQSQFKLSMSG-LIGGVSVSSINNFIVVVPPEKEQIR 200

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  +  +++  I  + + IE L+E+K  ++   VT+GL  +V M+DSG++W+G +P
Sbjct: 201 IVSYLDKKVSQLNEAIYIKQQQIERLRERKHVIIQQAVTQGLETNVPMQDSGVDWIGEIP 260

Query: 230 DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYE-TYQIVDP 288
            HW +  F  L T+ +R   +  +  + S   G +  +   R  G      E  YQ +  
Sbjct: 261 KHWGIVRFKNLFTQ-SRLPVRKGDGVVTSYRDGQVTLRSNRRVGGYTEAILEGGYQGIRK 319

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP---HGIDSTYLAWLMRSYDLCKV 345
           G++V   +D       +  +     G  T  Y+   P     +   Y A+L+R   L K 
Sbjct: 320 GQLVLNSMDAFEGAIGVSDSD----GKCTPEYVICDPINSVNVSQYYFAYLLREMALAKY 375

Query: 346 FYAMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
              + + +RQ    +++ ++  L ++VPP+KEQ DI + I  E+A++D  ++ + + I  
Sbjct: 376 IQVICNAVRQRAVRIRYNNLAPLFMVVPPVKEQEDIVSFIEKESAKLDAGIKHLNEQISK 435

Query: 403 LKERRSSFIAAAVTGQIDL 421
           LKE +++ I +AVTG+I +
Sbjct: 436 LKEYKTTLINSAVTGKIKV 454


>gi|134045681|ref|YP_001097167.1| restriction modification system DNA specificity subunit
           [Methanococcus maripaludis C5]
 gi|132663306|gb|ABO34952.1| restriction modification system DNA specificity domain
           [Methanococcus maripaludis C5]
          Length = 447

 Score =  130 bits (326), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 123/448 (27%), Positives = 207/448 (46%), Gaps = 42/448 (9%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT------SESGKDIIYIGLEDVESGTGKYL 64
           KDSG++WIG IP  W V  +K    LNTG +       E+G D +  G  D+ S   KY 
Sbjct: 6   KDSGIEWIGDIPADWGVKKLKYILGLNTGLSITKAELVENGVDCVNYG--DIHS---KYT 60

Query: 65  PKDGNSRQS---------DTSTVSIFAKGQILYGKLGPYLRKA----IIADFDG---ICS 108
               +SR +         DT+  +I ++G  ++      +  +     I + +       
Sbjct: 61  FDIVSSRDNLPKVPVEFIDTNPSAIASEGDFIFCDTSEDIEGSGNCLFIRESNNKPIFAG 120

Query: 109 TQFLVLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
           +  ++ +P   +     G+LL S D+  +I+    G  +     K + +I + +PP+ EQ
Sbjct: 121 SHTILGRPLINVNSTYLGYLLKSPDIKSQIQKRVVGIKVYSITQKILKSISLILPPVDEQ 180

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I + +  +  +ID++I +    I+  K  KQ++++  VTKGL+P V MKDSGIEW+G 
Sbjct: 181 QEIAQYLDDKVGQIDSIIEKTKSSIDEYKSYKQSIITETVTKGLDPTVTMKDSGIEWIGD 240

Query: 228 VPDHWEVKPFFALVTELN--RKNTKLIESNILSLSYGNIIQKLE----TRNMGLKPESYE 281
           +P+HW++     L T  N   K++    S    +SYG++ +  E       +    E  +
Sbjct: 241 IPEHWDIIKIRYLGTLQNGISKSSSYFGSGYPFVSYGDVYKNYELPKSVEGLVESNEFDK 300

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSA--QVMERGIITSAYMAVKPHG---IDSTYLAWL 336
           +   V+ G++ F       D+    +     M   +     +  +P     ++  Y  + 
Sbjct: 301 SNYSVEYGDVFFTRTSETIDEIGFTATCMHTMNDAVFAGFLIRFRPFDSKLLNPLYSKYY 360

Query: 337 MRSYDLCKVFYAMGSGL--RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
            RS D+ + F+     L  R SL  E +K+LPVLVPP  EQ  I   I      ID L+ 
Sbjct: 361 FRS-DMHRRFFVKEMNLVTRASLSQELLKKLPVLVPPHNEQIAIGKFIEETCQTIDQLIT 419

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           K +Q I  LK  + S I   VTG+ +++
Sbjct: 420 KKQQLITELKAYKKSLIYEVVTGKKEVK 447



 Score = 70.1 bits (170), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 109/221 (49%), Gaps = 17/221 (7%)

Query: 217 MKDSGIEWVGLVPDHWEVKPF---FALVTELNRKNTKLIESNILSLSYGNIIQK-----L 268
           MKDSGIEW+G +P  W VK       L T L+    +L+E+ +  ++YG+I  K     +
Sbjct: 5   MKDSGIEWIGDIPADWGVKKLKYILGLNTGLSITKAELVENGVDCVNYGDIHSKYTFDIV 64

Query: 269 ETR-NMGLKPESY---ETYQIVDPGEIVFRFI--DLQNDKRSLRSAQVMERGIITSAYMA 322
            +R N+   P  +       I   G+ +F     D++     L   +   + I   ++  
Sbjct: 65  SSRDNLPKVPVEFIDTNPSAIASEGDFIFCDTSEDIEGSGNCLFIRESNNKPIFAGSHTI 124

Query: 323 V-KPH-GIDSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDIT 379
           + +P   ++STYL +L++S D+         G++  S+  + +K + +++PP+ EQ +I 
Sbjct: 125 LGRPLINVNSTYLGYLLKSPDIKSQIQKRVVGIKVYSITQKILKSISLILPPVDEQQEIA 184

Query: 380 NVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
             ++ +  +ID ++EK + SI   K  + S I   VT  +D
Sbjct: 185 QYLDDKVGQIDSIIEKTKSSIDEYKSYKQSIITETVTKGLD 225


>gi|268325013|emb|CBH38601.1| putative type I restriction enzyme, DNA specificity subunit
           [uncultured archaeon]
          Length = 445

 Score =  130 bits (326), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 122/449 (27%), Positives = 202/449 (44%), Gaps = 47/449 (10%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K Y +YKDSG++WIG IP+HW+  PIK    +  G+          +  +D E    K  
Sbjct: 3   KPYLKYKDSGIEWIGEIPEHWEAKPIKYVGDIVLGKM---------LTPDDKEGYFRKPY 53

Query: 65  PKDGNSRQSDTSTVSI--------------FAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
            +  N       T  I                +  +L  + G   R AI  +    C  Q
Sbjct: 54  LRAQNITWEKVDTEDIKEMWFSEKELSQYRLKENDLLVSEGGEVGRTAIWQNELNECYIQ 113

Query: 111 FLVLQPKDVLPELLQGWLLSIDV---TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
             V +           +L    +   T   ++I    +++H   + +  I    P   EQ
Sbjct: 114 NSVHKITIKSKNNPHYYLYHFQIYGKTGYFDSIVNRVSIAHLTREKLKEIMFLSPTFHEQ 173

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I   +  +T +IDT I  + + I+LLKE++ A+++  VTKGLNP+VK+KDSGIEW+G 
Sbjct: 174 QTIANYLDRKTHQIDTFIENKQKLIDLLKEQRAAIINQAVTKGLNPNVKLKDSGIEWLGE 233

Query: 228 VPDHWEVKPF---FALV---TELNRKNTKLIESNILS------LSYGNIIQKLETRNMGL 275
           +P+HWE++     F L+   T    +N    E+  ++      L+ G I+ K   +    
Sbjct: 234 IPEHWELRKVGRSFNLIGSGTTPKSENIGYYENGTINWVITGDLNDG-ILDKTSKKITEK 292

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV--KPHGIDSTYL 333
             + Y T +I   G ++         K SL + +    G +  A  A+   P+  +    
Sbjct: 293 ALDEYSTLKIYPVGTLLIAMYGATIGKISLMNFE----GCVNQACCALSNSPYLSNEFSF 348

Query: 334 AWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
            W + +     +  + G G + ++  E V+ L +  PP  EQ  I   ++ +T RID L+
Sbjct: 349 YWFLANKQNI-INMSFGGG-QPNISQEVVRSLKIPTPPSSEQQAIIYHLDEQTTRIDKLM 406

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           E+  + I  LKE R++ I+  VTG+ID+R
Sbjct: 407 ERQGRQIEHLKEYRTTLISEVVTGKIDVR 435



 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 103/222 (46%), Gaps = 16/222 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSES-------GKDIIYIGLEDVESGTGK 62
           KDSG++W+G IP+HW++  + R F  + +G T +S          I ++   D+  G   
Sbjct: 224 KDSGIEWLGEIPEHWELRKVGRSFNLIGSGTTPKSENIGYYENGTINWVITGDLNDGILD 283

Query: 63  YLPKDGNSRQSDT-STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
              K    +  D  ST+ I+  G +L    G  + K  + +F+G  +     L     L 
Sbjct: 284 KTSKKITEKALDEYSTLKIYPVGTLLIAMYGATIGKISLMNFEGCVNQACCALSNSPYLS 343

Query: 122 -ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            E    W L+    Q I  +  G    +   + + ++ +P PP +EQ  I   +  +T R
Sbjct: 344 NEFSFYWFLA--NKQNIINMSFGGGQPNISQEVVRSLKIPTPPSSEQQAIIYHLDEQTTR 401

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
           ID L+  + R IE LKE +  L+S +VT  ++    ++D GI
Sbjct: 402 IDKLMERQGRQIEHLKEYRTTLISEVVTGKID----VRDYGI 439


>gi|71735008|ref|YP_272417.1| type I restriction-modification system specificity subunit
           [Pseudomonas syringae pv. phaseolicola 1448A]
 gi|71555561|gb|AAZ34772.1| type I restriction-modification system specificity subunit
           [Pseudomonas syringae pv. phaseolicola 1448A]
          Length = 448

 Score =  130 bits (326), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 124/428 (28%), Positives = 210/428 (49%), Gaps = 42/428 (9%)

Query: 23  KHWKVVPIKRFTKLNTGRTSES---GKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           K W++  +K    +N   +      G+   ++ +E V S  G+    +    ++  S  +
Sbjct: 23  KKWRICRLKHVALINPYLSLSRVRWGEPASFLPMEAV-SADGQVDYSEPKDSKNLVSGFT 81

Query: 80  IFAKGQILYGKLGPYL---RKAIIADFD---GICSTQFLVLQP-KDVLPELLQGWLLSID 132
            F  G ++  K+ P     + A+++D     G  ST+F VL+  K  +P  +     S  
Sbjct: 82  NFEAGDVILAKITPCFENGKGAVLSDMPTRVGFGSTEFHVLRANKKAIPNFIYYITKSDL 141

Query: 133 VTQRIEAICEG-ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
             ++ EA+  G A         + N  + +P L EQ  I + +  +T  I   I+++   
Sbjct: 142 FMRQGEALMIGSAGQKRVSTSYVENFQLALPSLHEQRKIVDFLEEKTSLIAQAISKKEHQ 201

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV---KPFFALVTELNRKN 248
           IELL+E+KQ LV   VT+GL+P   M+++GIEW+G +P HWEV   K  FA   EL RKN
Sbjct: 202 IELLEERKQILVQQAVTRGLDPASPMRNAGIEWIGEIPKHWEVRRSKFTFAQRKELARKN 261

Query: 249 TKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVF-----RFIDLQNDKR 303
              + +   + SYG I Q      +G K        +V   +I+F     + +++ +   
Sbjct: 262 DIQLSA---TQSYGVIPQDEYEEKVGRK--------VV---KILFNLEKRKHVEVDDFVI 307

Query: 304 SLRSAQ-VMER----GIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFYAMGSGLR--Q 355
           S+RS Q  +ER    G I S+Y+ +KP  GID  Y ++L++S        A  + +R  Q
Sbjct: 308 SMRSFQGGLERAWASGCIRSSYVILKPLPGIDPDYYSYLLKSKRYIAALQATANFIRDGQ 367

Query: 356 SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAV 415
            L FE+   + + +PP+ EQ +I   +    ++ D  +  +EQ I  LKE +++ I +AV
Sbjct: 368 DLNFENFALVDLPIPPLDEQKEIARYLASWLSKADRSLYLLEQQITKLKEYKATLINSAV 427

Query: 416 TGQIDLRG 423
           TG+I + G
Sbjct: 428 TGKIKVPG 435


>gi|299141338|ref|ZP_07034475.1| type I restriction-modification system specificity determinant
           [Prevotella oris C735]
 gi|298577298|gb|EFI49167.1| type I restriction-modification system specificity determinant
           [Prevotella oris C735]
          Length = 407

 Score =  130 bits (326), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 108/434 (24%), Positives = 200/434 (46%), Gaps = 45/434 (10%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDII-----YIGLEDVESG 59
           + Y  YKDSG QW+G IP HW++   K F    T R S+ G + +     Y G+ +    
Sbjct: 2   QTYDSYKDSGEQWLGRIPSHWEIRRSK-FLWKETDRRSQKGTEQLLSVSQYDGVREA--- 57

Query: 60  TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV 119
                  +  SR           K + +   +  +L    +++F+G+ S  + V   KD 
Sbjct: 58  -------NAESRSESLVGYKYVHKDEFVINIMLAWLGGLGVSNFEGVVSPAYCVYHLKDK 110

Query: 120 LPELLQGWLLSIDVTQRIEAICEGAT-MSHADWK----GIGNIPMPIPPLAEQVLIREKI 174
                  +L      Q +      +T +  + W+      G++   +PP+ EQ  + + +
Sbjct: 111 QNPRFLHYLYR--TPQYLAEFARHSTGIVPSRWRMYTDDFGDVLTILPPIEEQNRMVQYL 168

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             +T +ID +I ++ + I+LL E+KQ +++  VTKGL+P+V MKDSGI+W+G +P+HWE+
Sbjct: 169 DEQTSQIDEVIAQQQKMIDLLNERKQIIINNAVTKGLDPNVSMKDSGIDWIGKMPNHWEL 228

Query: 235 KPFFALVTELNRKNTKLI-----ESNILSLSYG--NIIQKLETRNMGLKPESYETYQIVD 287
           K +  L    +     +        N +   YG   +I K++  N+  K          D
Sbjct: 229 KQYKYLFYNFDNLRKPITADQRSRDNPMYDYYGASGVIDKIDYYNIDDKVLLIGE----D 284

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFY 347
              ++ R + L    +         +  + +    +KP   +  ++A +M + D     +
Sbjct: 285 GANLLMRNLPLVYKAKG--------KFWVNNHAHILKPIKDNYDFMALVMEAADYT--LF 334

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
             GS  +  L   ++  + + +PPI+EQ  I N +N     +D  ++K ++ + LL+ER+
Sbjct: 335 ITGSA-QPKLSQANLNSVKLPIPPIEEQEKIVNFVNENAGILDFPLKKAKKQVELLQERK 393

Query: 408 SSFIAAAVTGQIDL 421
              I   VTG+I++
Sbjct: 394 QIIINEVVTGKINV 407


>gi|284052081|ref|ZP_06382291.1| restriction modification system DNA specificity subunit
           [Arthrospira platensis str. Paraca]
 gi|78773866|gb|ABB51216.1| type I RM system S subunit [Arthrospira platensis]
          Length = 392

 Score =  129 bits (324), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 146/272 (53%), Gaps = 19/272 (6%)

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           IPPL EQ  I   +  ET +ID LI  + R + LL EK++AL+++ VT+GLNPDV M+DS
Sbjct: 124 IPPLGEQKAIAHYLDIETAKIDQLIKAKKRLLALLDEKRRALITHAVTRGLNPDVPMRDS 183

Query: 221 GIEWVGLVPDHWEVKPFFALVTELNRKNTKLI--ESNILSLSYGNIIQ-KLETRNMGLKP 277
           G+EW+G +P HWE+ P   ++  ++   ++ +  E NI  L  G++ + ++   N+G   
Sbjct: 184 GVEWIGEIPKHWEILPLRRILQTMDYGISESVGSEGNIAVLRMGDVDEGEISYDNVGFV- 242

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGI---ITSAYMAVKPHGIDST--- 331
           +  +   I+   +++F   +  N    +    +        ++ A   V+    DS    
Sbjct: 243 DDVDHDLILKANDLLF---NRTNSLDKIGKVAIFRNNFLFPVSFASYLVRMRCNDSVIPE 299

Query: 332 YLAWLMRSYDLCKVFYAMGSGL----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETA 387
           YL +L+ S  L  + +A  + L    + +L       + + +PPI+EQ +IT  I   T 
Sbjct: 300 YLNYLLNS--LPVLTWAKSNALPAIGQVNLNPNRYSYIKIPIPPIEEQLNITEYIQTNTK 357

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           +I  L    E++I LL+ERR+S I AAVTGQI
Sbjct: 358 KIKKLCLSSEETIKLLQERRTSLITAAVTGQI 389



 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 99/209 (47%), Gaps = 14/209 (6%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTSESGK--DIIYIGLEDVESGTGKYLPKD 67
           +DSGV+WIG IPKHW+++P++R  + ++ G +   G   +I  + + DV+ G   Y   D
Sbjct: 181 RDSGVEWIGEIPKHWEILPLRRILQTMDYGISESVGSEGNIAVLRMGDVDEGEISY---D 237

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG-----ICSTQFLV-LQPKD-VL 120
                 D     I     +L+ +     +   +A F       +    +LV ++  D V+
Sbjct: 238 NVGFVDDVDHDLILKANDLLFNRTNSLDKIGKVAIFRNNFLFPVSFASYLVRMRCNDSVI 297

Query: 121 PELLQGWLLSIDVTQRIEAICEGAT-MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
           PE L   L S+ V    ++    A    + +      I +PIPP+ EQ+ I E I   T 
Sbjct: 298 PEYLNYLLNSLPVLTWAKSNALPAIGQVNLNPNRYSYIKIPIPPIEEQLNITEYIQTNTK 357

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVT 208
           +I  L       I+LL+E++ +L++  VT
Sbjct: 358 KIKKLCLSSEETIKLLQERRTSLITAAVT 386



 Score = 45.8 bits (107), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 328 IDST----YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
           ID+T    +L WL        +           L  +D     V +PP+ EQ  I + ++
Sbjct: 79  IDATTTHHHLRWLFYLLQTLNLDQGTDEAAVPGLSRDDAYAKKVFIPPLGEQKAIAHYLD 138

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           +ETA+ID L++  ++ + LL E+R + I  AVT
Sbjct: 139 IETAKIDQLIKAKKRLLALLDEKRRALITHAVT 171


>gi|304315216|ref|YP_003850363.1| type I restriction-modification enzyme, subunit S
           [Methanothermobacter marburgensis str. Marburg]
 gi|302588675|gb|ADL59050.1| predicted type I restriction-modification enzyme, subunit S
           [Methanothermobacter marburgensis str. Marburg]
          Length = 435

 Score =  129 bits (324), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 116/448 (25%), Positives = 208/448 (46%), Gaps = 56/448 (12%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTG------RTSESGKDIIYIGLEDVES 58
           K YP+YKDSGV+WIG IP  W V   K   K   G      R + SG  + Y+ ++ +  
Sbjct: 4   KPYPEYKDSGVEWIGEIPCGWNVHRFKIHFKYIKGKVPKDLRETPSGDSLPYLTMDYLRG 63

Query: 59  GTGK--YLPKDGNS-RQSDTSTVSIF---AKGQILYGK---LGPYLRKAIIADFDGICST 109
              K  Y   DG + R +D   + ++     G+ L GK   L   + K I+++ D +  +
Sbjct: 64  RESKVFYCDSDGGAVRVNDGDLLLLWDGSNAGEFLEGKDGYLSSTMVKLIVSEMD-LGYS 122

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
           ++L    + +L +L                   G  + H     +  I +P P L EQ  
Sbjct: 123 KYLCKAFEPLLKDL-----------------TTGMGIPHVKDNVLATIRIPYPSLEEQRK 165

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   + ++  +ID  I +  R I+LL+EK+ AL++  VTKGLNP+VKMK SG++W+G +P
Sbjct: 166 IASFLDSKISKIDLTIEKYTRLIDLLQEKRNALINQAVTKGLNPNVKMKYSGVKWIGEIP 225

Query: 230 DHWEVKPF---FALV-----------TELNRKNTKLIESNILSLSYGNIIQKLETRNMGL 275
            +WE++     F ++           +  NR     + +  L+ S   I+ +   R    
Sbjct: 226 QNWELRKISRSFEIIGSGTTPKSQDGSYYNRGTIPWVITGDLNDS---ILNETSKRITKK 282

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTY-LA 334
               Y   +I     ++         K SL +   ++  +  +  +    + +D  +   
Sbjct: 283 ALRDYSALKIYKKNSLIVAMYGATIGKISLLN---IDACVNQACCVLSNSNILDIKFVFY 339

Query: 335 WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           W   + D   +      G + ++    +K L + VPP+KEQ  I + ++  +++I++  +
Sbjct: 340 WFFSNRD--NIISLSDGGGQPNISQHVIKNLRIQVPPLKEQKIIVSYLDQNSSKINLTTK 397

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           KI++++ LLKE + S I   VTG++D++
Sbjct: 398 KIQKNVDLLKEYKKSLIYHLVTGKVDVK 425


>gi|57506069|ref|ZP_00371992.1| type I restriction-modification system specificity subunit,
           putative [Campylobacter upsaliensis RM3195]
 gi|57015677|gb|EAL52468.1| type I restriction-modification system specificity subunit,
           putative [Campylobacter upsaliensis RM3195]
          Length = 427

 Score =  129 bits (324), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 111/442 (25%), Positives = 215/442 (48%), Gaps = 61/442 (13%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYI---GLEDVESGTGKYLPKDGNSRQSDT 75
           G IP HW+V  +K    ++   + +   +++ +   G+ + +  T K     G   Q+  
Sbjct: 6   GKIPAHWEVRRLKYLFYISKEESRDEFPNVLSLTQNGIIERDITTNK-----GQLAQNYI 60

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP-ELLQGWLLSIDVT 134
              +I  +G I+   +         + F+G+ S  ++ ++P + L     + +  ++   
Sbjct: 61  G-YNIVKRGDIILNPMDLSSGYVAKSTFEGVISQAYIKIRPLETLNLSYYENFFQNLYHY 119

Query: 135 QRIEAICEGATMSHADWKG---IGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
           + +  + +G +  H    G     NI +P+PPL EQ  I E +  +  +I   I ++ + 
Sbjct: 120 KILWHLGKGISYDHRWTLGNDVFLNIKIPLPPLQEQKEIAEFLDKKCEKIQNYINKKQKL 179

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKL 251
           I LL+EKKQAL++  +TKGLNP+++ K+SGIEW+G +P HWE+K     + E+       
Sbjct: 180 ITLLQEKKQALINEAITKGLNPNIEFKNSGIEWLGEIPKHWEIKK-LKYIGEI------- 231

Query: 252 IESNILSLSYGNIIQK-LETRNMGLKP--ESYETY------QIVDPGEIVFRFID----- 297
                    +G +I K ++  +   KP  + Y T+       I++P  + + FID     
Sbjct: 232 ---------FGGVIGKTIKDFSKEYKPNFKPYITFTNVCNNAIINPNSMEYVFIDFDEKQ 282

Query: 298 ---LQNDKRSLRSAQVMERGIITSAYMA---------VKPHGIDS----TYLAWLMRSYD 341
              L+ND   L+S++  E    ++ Y+           K   I+      YL +L+ S  
Sbjct: 283 NKVLKNDILFLQSSETFEDVGKSAIYLNDDEVYLNTFCKGFRIEREAYPMYLNYLLSSLS 342

Query: 342 LCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
             + F ++ SG  R +L+ E    +P+++PP++EQ +I   ++ +  +I+  +EK ++ I
Sbjct: 343 YKRYFMSVCSGFTRINLRQEHFLDIPLILPPLQEQKEIAEFLDEKCKKINSAIEKTKKQI 402

Query: 401 VLLKERRSSFIAAAVTGQIDLR 422
             ++E +++ I  AV G+I L+
Sbjct: 403 EFVREYKNTLINEAVCGRIKLK 424



 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/218 (23%), Positives = 99/218 (45%), Gaps = 21/218 (9%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDII---------YIGLEDV--- 56
           ++K+SG++W+G IPKHW++  +K   ++  G   ++ KD           YI   +V   
Sbjct: 204 EFKNSGIEWLGEIPKHWEIKKLKYIGEIFGGVIGKTIKDFSKEYKPNFKPYITFTNVCNN 263

Query: 57  ---ESGTGKYLPKDGNSRQSDTSTVSI-FAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
                 + +Y+  D + +Q+      I F +    +  +G   + AI  + D +    F 
Sbjct: 264 AIINPNSMEYVFIDFDEKQNKVLKNDILFLQSSETFEDVG---KSAIYLNDDEVYLNTFC 320

Query: 113 --VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
                 ++  P  L   L S+   +   ++C G T  +   +   +IP+ +PPL EQ  I
Sbjct: 321 KGFRIEREAYPMYLNYLLSSLSYKRYFMSVCSGFTRINLRQEHFLDIPLILPPLQEQKEI 380

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            E +  +  +I++ I +  + IE ++E K  L++  V 
Sbjct: 381 AEFLDEKCKKINSAIEKTKKQIEFVREYKNTLINEAVC 418


>gi|188535437|ref|YP_001909234.1| type I restriction-modification system, specifity subunit [Erwinia
           tasmaniensis Et1/99]
 gi|188030479|emb|CAO98373.1| type I restriction-modification system, specifity subunit [Erwinia
           tasmaniensis Et1/99]
          Length = 435

 Score =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 123/455 (27%), Positives = 213/455 (46%), Gaps = 57/455 (12%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKL--NTGRTSESGKDIIYIGLEDVES 58
           M     Y  YK+S + WI  IP  W+   +KRF  +       S++GK+ + + L    S
Sbjct: 4   MAELPKYEAYKESCLNWIDTIPYDWE---LKRFKYILDEINLRSKTGKETL-LSL----S 55

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAK----GQILYGKLGPYLRKAIIADFDGICSTQFLVL 114
                LPKD    +S  +   +  K      ++  K+        ++  +GI S  + V 
Sbjct: 56  KYNGVLPKDSLEERSGCAETLVGYKRVGIKDLVINKMQAVNGLLAVSRIEGITSPDYSVY 115

Query: 115 QPKD--VLPELLQGWLLSI-----DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
           + K+  +L     G+LL       +  +R+  + EG    + +   + +I   +P +  Q
Sbjct: 116 RSKNNLILNIDFLGYLLLQPEYIGEFKKRVTGVMEGFIRLYTE--DLYSIHAILPDVKTQ 173

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
            +I + +  ++ +ID  I  + + I LLKE+KQ ++   VT+GL+P+V+MKDSG++W+G 
Sbjct: 174 FIIVKYLDKKSAQIDEAIKIKQQQITLLKERKQIIIQKAVTQGLDPNVQMKDSGVDWIGK 233

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
           +P HWE++    L T+   K            +  + +Q   T+  G+ P+  E Y+ + 
Sbjct: 234 IPVHWEIRRSKFLFTQRKEK------------ALNDDVQLSATQAYGVIPQ--EKYEALT 279

Query: 288 PGEIVFRFIDLQNDKR----------SLRSAQ-VMER----GIITSAYMAVKP-HGIDST 331
              +V   I    DKR          S+RS Q  +ER    G I S+Y+ +K    ID  
Sbjct: 280 GKRVV--KIQFHLDKRKHVEKDDFVISMRSFQGGLERAWSCGCIRSSYVVLKALQNIDPL 337

Query: 332 YLAWLMRSYDLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           +  +L++            S +R  Q L F++  R+ + +PP++EQ  I N +       
Sbjct: 338 FYGYLLKLPSYIAALQQTASFIRDGQDLNFDNFSRVDLFIPPLEEQTAIANYVESFLTSS 397

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           D  +  IEQ I  LKE +++ I +AVTG+I +  E
Sbjct: 398 DEAMNLIEQQIEKLKEYKTTLINSAVTGKIKITPE 432


>gi|303242151|ref|ZP_07328641.1| restriction modification system DNA specificity domain protein
           [Acetivibrio cellulolyticus CD2]
 gi|302590338|gb|EFL60096.1| restriction modification system DNA specificity domain protein
           [Acetivibrio cellulolyticus CD2]
          Length = 638

 Score =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 117/443 (26%), Positives = 206/443 (46%), Gaps = 50/443 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG---------LEDVESGTG 61
           KDSG++WIG IP+ W+ + IK  + +  G +     + IY           + DV     
Sbjct: 6   KDSGIEWIGEIPQEWETIKIKYLSPVLRGASPRPIDNPIYFNENGEYVWTRIADVSKCNR 65

Query: 62  ------KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
                 +Y+   G S+       S+        GK  P + K      DG     F +L 
Sbjct: 66  YFEKYYEYMSDLGTSKSIKIEPNSLIVSICATVGK--PIITKVKCCIHDGF--VYFPLLD 121

Query: 116 PK--DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
           PK  D L  +                + +  T  + + + +G+I +PI   +E   I + 
Sbjct: 122 PKYNDFLYYIFNN-------GSCFAGLGKLGTQLNLNTETVGSISIPIIDDSELKSIIKY 174

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  +   ID ++      I+  K+ KQ++++  VTKGLNP V+MKDSGIEW   +P HW+
Sbjct: 175 LDEKCSEIDNIVENTKASIDEYKKYKQSVITEAVTKGLNPSVEMKDSGIEWNRHIPLHWK 234

Query: 234 V---KPFFALVTELNRKNTKLIESNILSLS--YGNIIQ----KLETRNMGLKPESYETYQ 284
           V   +  F L     RK+  + E   L+ S  YG + Q    +LE + +    + ++  +
Sbjct: 235 VVNGRRLFEL-----RKDKAMPEDRQLTASQKYGIMYQDEFMQLENQRVVTVQKDFDILK 289

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH-GIDSTYLAWLMRSYDLC 343
            V+P + V   I +++ +  L  +Q+  RG I+SAY+ + P+  +   Y  WL +S    
Sbjct: 290 HVEPNDFV---ISMRSFQGGLEYSQL--RGCISSAYVMLIPNEKVYCPYFRWLFKSVKYI 344

Query: 344 KVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
               +  + +R  Q+++F +  ++P+ + PI EQ  I + +N + A ID ++ K +Q + 
Sbjct: 345 NALQSTSNLVRDGQAMRFSNFVQIPLFLIPIDEQKRIADYLNAKCAEIDNIISKKQQIVT 404

Query: 402 LLKERRSSFIAAAVTGQIDLRGE 424
            L+  + S I   VTG+  ++ E
Sbjct: 405 ELENYKKSLIYECVTGKRSVQTE 427



 Score = 38.5 bits (88), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 49/208 (23%), Positives = 85/208 (40%), Gaps = 11/208 (5%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNII--QKLETRNMG 274
           MKDSGIEW+G +P  WE      L   L   + + I++ I     G  +  +  +     
Sbjct: 5   MKDSGIEWIGEIPQEWETIKIKYLSPVLRGASPRPIDNPIYFNENGEYVWTRIADVSKCN 64

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI-----D 329
              E Y  Y + D G    + I ++ +   +     + + IIT     +    +     D
Sbjct: 65  RYFEKYYEY-MSDLG--TSKSIKIEPNSLIVSICATVGKPIITKVKCCIHDGFVYFPLLD 121

Query: 330 STYLAWLMRSYDLCKVFYAMGS-GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
             Y  +L   ++    F  +G  G + +L  E V  + + +    E   I   ++ + + 
Sbjct: 122 PKYNDFLYYIFNNGSCFAGLGKLGTQLNLNTETVGSISIPIIDDSELKSIIKYLDEKCSE 181

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           ID +VE  + SI   K+ + S I  AVT
Sbjct: 182 IDNIVENTKASIDEYKKYKQSVITEAVT 209


>gi|88811656|ref|ZP_01126910.1| type I restriction-modification system specificity subunit
           [Nitrococcus mobilis Nb-231]
 gi|88791047|gb|EAR22160.1| type I restriction-modification system specificity subunit
           [Nitrococcus mobilis Nb-231]
          Length = 710

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 115/435 (26%), Positives = 200/435 (45%), Gaps = 26/435 (5%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKR-FTKL-NTGRTSESGKDI-IYIGL---EDVES 58
           K YP+YK +   W+G IP+HW V+P +  F ++ + G   E    + I  G+   + +  
Sbjct: 251 KPYPEYKPTAQAWLGEIPQHWSVLPNRALFNEVKDRGHPDEEMLSVTITKGIVRQKALLE 310

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK- 117
           G+ K      +S   D S   +     I Y K+  +      +   GI S  ++V++ + 
Sbjct: 311 GSSKK-----DSSNLDKSAYKLVQPRDIAYNKMRAWQGAIGASALRGIISPAYVVMRLRN 365

Query: 118 -DVLPELLQGWLLSIDVTQRIEAICEGAT--MSHADWKGIGNIPMPIPPLAEQVLIREKI 174
            D LP  +     +    +  E    G T  M     +    I  P PP AEQ  I   +
Sbjct: 366 GDDLPSYIHYLYRTPQFAKEAERWSYGITSDMWSLRPEHFKMIYTPEPPTAEQEAIVRFL 425

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
                R++     + + I LL E+KQA++   VT+GL+  V +K SGI W+G +P HWEV
Sbjct: 426 DWANGRLERATRAKRKVIALLNEQKQAIIHQAVTRGLDSSVPLKPSGIPWLGHIPRHWEV 485

Query: 235 KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFR 294
           K    L+ E++ ++T   E  +    +  ++   E  +   +  +   ++IV PG+ V  
Sbjct: 486 KRIKYLLREVDERSTTGSEPLLSMRMHHGLVLFAEHFSRPPQAATLVGFKIVHPGQFVVN 545

Query: 295 FIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYA----M 349
            +   N    +  A  +  G+++  Y    P G  +  +L  L RS  +   F A    +
Sbjct: 546 RMQAGN---GVIFASTLT-GLVSPDYAVFDPIGDANVDFLGELFRSRKVRAKFRAESKGL 601

Query: 350 GSGLRQSLKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
           G+G    L+   + +  + V +PP  EQ DI   +  E + ++  + ++E  I LL+E R
Sbjct: 602 GTGTSGFLRLYNDRLGAIHVALPPRAEQGDIVAGLTRELSEVNTTISRLESEIELLREYR 661

Query: 408 SSFIAAAVTGQIDLR 422
           +  +A  VTG++D+R
Sbjct: 662 TRLVADVVTGKLDVR 676



 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 94/220 (42%), Gaps = 16/220 (7%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L P  + K +   W+G +P HW V P  AL  E+  +     E   ++++ G + QK   
Sbjct: 250 LKPYPEYKPTAQAWLGEIPQHWSVLPNRALFNEVKDRGHPDEEMLSVTITKGIVRQKALL 309

Query: 271 RNMGLKPESY---ETYQIVDPGEIVFRFIDLQNDKRSLRSA--QVMERGIITSAYMAVKP 325
                K  S      Y++V P +I +      N  R+ + A      RGII+ AY+ ++ 
Sbjct: 310 EGSSKKDSSNLDKSAYKLVQPRDIAY------NKMRAWQGAIGASALRGIISPAYVVMRL 363

Query: 326 HGIDS--TYLAWLMRSYDLCKVFYAMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITN 380
              D   +Y+ +L R+    K       G+     SL+ E  K +    PP  EQ  I  
Sbjct: 364 RNGDDLPSYIHYLYRTPQFAKEAERWSYGITSDMWSLRPEHFKMIYTPEPPTAEQEAIVR 423

Query: 381 VINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            ++    R++       + I LL E++ + I  AVT  +D
Sbjct: 424 FLDWANGRLERATRAKRKVIALLNEQKQAIIHQAVTRGLD 463


>gi|56459752|ref|YP_155033.1| restriction endonuclease S subunit [Idiomarina loihiensis L2TR]
 gi|56178762|gb|AAV81484.1| Restriction endonuclease S subunit [Idiomarina loihiensis L2TR]
          Length = 448

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 126/427 (29%), Positives = 198/427 (46%), Gaps = 47/427 (11%)

Query: 21  IPKHWKVVPIKRFTKLNTGRT------SESGKDIIYI--------GLEDVESGTGKYLPK 66
           +P+ WK++ +K    + TG         E+G  +I I         L +++      L K
Sbjct: 20  LPERWKLIKLKLVCNIETGFAFPSEVFGETGTPVIRITDIKNREINLSEIKR-VDDLLLK 78

Query: 67  DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
               R S      I A      GK+G Y      +D     + +     P  +    L  
Sbjct: 79  SKPKRPSVNKGDIIMAMTGATIGKVGYY-----NSDKPSYLNQRVCRFIPASIDRGYLWH 133

Query: 127 WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL-AEQVLIREKIIAETVRIDTLI 185
            L S    + IE    G   ++     + N P P+P L AEQ  I + +  ET +ID LI
Sbjct: 134 TLNSEIYKKYIELEAFGGAQANISDSQLLNFPAPLPELEAEQQKIAQFLDYETAKIDALI 193

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF-FA--LVT 242
            E+ R IELLKEK+QA++S+ VTKGLNPD  MKDSGIEW+G VP+HWE+K   F   +++
Sbjct: 194 DEQKRLIELLKEKRQAVISHAVTKGLNPDAPMKDSGIEWLGEVPEHWEIKKLKFCSRMLS 253

Query: 243 ELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDK 302
           +  + NT  I    +    G  I+               T    D   ++F  +D+   K
Sbjct: 254 DKGKDNTNAISLENIENGTGAFIK---------------TESNFDQEGVLFEPLDILFGK 298

Query: 303 RSLRSAQVM---ERGIITSAYMAVKPH-GIDSTYLAWLMRSYDLCKVF--YAMGSGLRQS 356
                A+V    E G      +  + +  I   +L + + S +  +     + GS + ++
Sbjct: 299 LRPYLAKVYLAREHGSALGDILVFRANKDISPEFLFFRLISQEFIRQVDQSSYGSKMPRA 358

Query: 357 LKFEDVKRLPVLVPPIKEQFDITNVI-NVETARIDVLVEKIEQSIVLLKERRSSFIAAAV 415
              E +K L + VPPI+EQ  +++ + N++  +I   V      + LL+ERRS+ I+AAV
Sbjct: 359 -NPELIKSLQIAVPPIEEQVKVSDYLANLQFNKIMPSVINASSLVKLLEERRSALISAAV 417

Query: 416 TGQIDLR 422
           TG+ID+R
Sbjct: 418 TGKIDVR 424



 Score = 97.4 bits (241), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 111/201 (55%), Gaps = 11/201 (5%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD-IIYIGLEDVESGTGKYLPKDGN 69
           KDSG++W+G +P+HW++  +K  +++     S+ GKD    I LE++E+GTG ++  + N
Sbjct: 226 KDSGIEWLGEVPEHWEIKKLKFCSRM----LSDKGKDNTNAISLENIENGTGAFIKTESN 281

Query: 70  SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWL 128
             Q       +F    IL+GKL PYL K  +A   G      LV +  KD+ PE L   L
Sbjct: 282 FDQEGV----LFEPLDILFGKLRPYLAKVYLAREHGSALGDILVFRANKDISPEFLFFRL 337

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA-ETVRIDTLITE 187
           +S +  ++++    G+ M  A+ + I ++ + +PP+ EQV + + +   +  +I   +  
Sbjct: 338 ISQEFIRQVDQSSYGSKMPRANPELIKSLQIAVPPIEEQVKVSDYLANLQFNKIMPSVIN 397

Query: 188 RIRFIELLKEKKQALVSYIVT 208
               ++LL+E++ AL+S  VT
Sbjct: 398 ASSLVKLLEERRSALISAAVT 418


>gi|260557402|ref|ZP_05829617.1| restriction endonuclease S subunit [Acinetobacter baumannii ATCC
           19606]
 gi|260409028|gb|EEX02331.1| restriction endonuclease S subunit [Acinetobacter baumannii ATCC
           19606]
          Length = 451

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 127/456 (27%), Positives = 200/456 (43%), Gaps = 72/456 (15%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSES------GKDIIYIGLEDVESG------TGKYLP 65
           +G +P HW +  +KR+  +  G    S      G  +I IG  D+++         KY+P
Sbjct: 1   MGVVPSHWIITTLKRYCYVKGGFAFSSDAFIDTGYPVIRIG--DIKTDGSINLENCKYIP 58

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQ 125
           +       D     +  K Q+L    G  + KA +       S Q   L  +    ELL 
Sbjct: 59  ESLAVNSRD----YLVEKNQLLMAMTGATIGKAGL-----YTSNQPAFLNQRVGKFELLA 109

Query: 126 G--------WLLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
                    ++L  D  Q  I+    G    +     + + P  IP   EQ  I   +  
Sbjct: 110 QNMNYRYLWYILKTDGYQEYIKLTAFGGAQPNISDTAMVDYPATIPSFDEQTQIANFLDH 169

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           ET +ID LI ++ + IELLKEK+QA++S+ VTKGL+P+V MKDSG+ W+G VP+HW++ P
Sbjct: 170 ETSKIDHLIEKQQKLIELLKEKRQAVISHAVTKGLDPNVPMKDSGVAWLGEVPEHWDITP 229

Query: 237 FFALVT------------ELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETY- 283
              L+             EL+      +E+ I  L   NI      RN  L  E  +   
Sbjct: 230 IRNLIRSGNLILQDGNHGELHPTANDYVETGIPFLMANNI------RNGNLFMEDVKRIP 283

Query: 284 -QIVDPGEIVF-RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYD 341
             + D   I F +  D+    +       +    I   Y  + P     TY  W  + + 
Sbjct: 284 KHLADTLRIGFAKAGDMLLTHKGTVGEVALVPQDIKEDYWMLTPQ---VTYYRWQGKKF- 339

Query: 342 LCKVFYA--MGSGLRQSLKFEDVKR-------------LPVLVPPIKEQFDITNVINVET 386
           L K FY     S ++  L+    K+             L V +PP  EQ +I++ I  + 
Sbjct: 340 LNKYFYYQFQSSSIQTQLEIIGAKQSTRAYVGLIAQGDLIVAIPPSHEQLEISSYILEKD 399

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
               +++ K + +I L++ERR++ I+AAVTG+ID+R
Sbjct: 400 QSYQLMIAKAQTAIQLMQERRTALISAAVTGKIDVR 435



 Score = 53.1 bits (126), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 54/225 (24%), Positives = 95/225 (42%), Gaps = 33/225 (14%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKL--------NTGRTSESGKDIIYIGL-----EDVE 57
           KDSGV W+G +P+HW + PI+   +         N G    +  D +  G+      ++ 
Sbjct: 211 KDSGVAWLGEVPEHWDITPIRNLIRSGNLILQDGNHGELHPTANDYVETGIPFLMANNIR 270

Query: 58  SGT-----GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII-----ADFDGIC 107
           +G       K +PK      +DT  +     G +L    G     A++      D+  + 
Sbjct: 271 NGNLFMEDVKRIPK----HLADTLRIGFAKAGDMLLTHKGTVGEVALVPQDIKEDYWMLT 326

Query: 108 -STQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGI---GNIPMPIPP 163
               +   Q K  L +       S  +  ++E I  GA  S   + G+   G++ + IPP
Sbjct: 327 PQVTYYRWQGKKFLNKYFYYQFQSSSIQTQLEII--GAKQSTRAYVGLIAQGDLIVAIPP 384

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             EQ+ I   I+ +      +I +    I+L++E++ AL+S  VT
Sbjct: 385 SHEQLEISSYILEKDQSYQLMIAKAQTAIQLMQERRTALISAAVT 429


>gi|313896063|ref|ZP_07829617.1| conserved hypothetical protein [Selenomonas sp. oral taxon 137 str.
           F0430]
 gi|320529368|ref|ZP_08030456.1| conserved domain protein [Selenomonas artemidis F0399]
 gi|312975488|gb|EFR40949.1| conserved hypothetical protein [Selenomonas sp. oral taxon 137 str.
           F0430]
 gi|320138334|gb|EFW30228.1| conserved domain protein [Selenomonas artemidis F0399]
          Length = 223

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 75/209 (35%), Positives = 119/209 (56%), Gaps = 8/209 (3%)

Query: 218 KDSGIEWVGLVPDHW---EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMG 274
           K +   W+  VP HW   + K  FA  TE N+ N    E NILSL+   +++    + +G
Sbjct: 8   KTTDQSWLTNVPKHWGYVKCKTLFATQTEKNKNNE---EGNILSLTLQGVVRNNREKPIG 64

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH-GIDSTYL 333
           L P  Y TYQI +  ++VF+ IDL+N   S R   V ERGI++SAY+ +     I++ Y 
Sbjct: 65  LSPSDYRTYQIFEKDDLVFKLIDLENISTS-RVGLVPERGIMSSAYIRLSAKCDINTRYF 123

Query: 334 AWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
            +      L ++F  +G+G+RQ+L   D+  + ++VPP  EQ  I   ++ + + ID  +
Sbjct: 124 YFQYYDLWLRQIFNGLGAGVRQTLSANDLLNIKIVVPPRDEQDQIVRYLDSKISAIDAGI 183

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            K+E+ I  LKE +S+ I+  VTG+ID+R
Sbjct: 184 SKLEEQIKCLKELKSTLISDVVTGKIDVR 212



 Score = 44.7 bits (104), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 94/217 (43%), Gaps = 20/217 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRF--TKLNTGRTSESGKDIIYIGLEDVES 58
           MK YK Y   K +   W+  +PKHW  V  K    T+    + +E G +I+ + L+ V  
Sbjct: 1   MKRYKTY---KTTDQSWLTNVPKHWGYVKCKTLFATQTEKNKNNEEG-NILSLTLQGVVR 56

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLG----PYLRKAIIADFDGICSTQFLVL 114
              +   K      SD  T  IF K  +++  +        R  ++ +  GI S+ ++ L
Sbjct: 57  NNRE---KPIGLSPSDYRTYQIFEKDDLVFKLIDLENISTSRVGLVPE-RGIMSSAYIRL 112

Query: 115 QPK-DVLPELLQGWLLSIDVTQRIEAICEGA--TMSHADWKGIGNIPMPIPPLAEQVLIR 171
             K D+           + + Q    +  G   T+S  D   + NI + +PP  EQ  I 
Sbjct: 113 SAKCDINTRYFYFQYYDLWLRQIFNGLGAGVRQTLSAND---LLNIKIVVPPRDEQDQIV 169

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             + ++   ID  I++    I+ LKE K  L+S +VT
Sbjct: 170 RYLDSKISAIDAGISKLEEQIKCLKELKSTLISDVVT 206


>gi|315124281|ref|YP_004066285.1| putative type I restriction enzyme specificity protein
           [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
 gi|315018003|gb|ADT66096.1| putative type I restriction enzyme specificity protein
           [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
          Length = 393

 Score =  127 bits (320), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 115/398 (28%), Positives = 176/398 (44%), Gaps = 44/398 (11%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK-----DIIYIGLEDVESGTGKY 63
            +K+SG++W+G IP+HW+VV I +      G   E+       +I  I + D++     Y
Sbjct: 3   NFKESGIEWLGEIPEHWEVVKINKIVTFVNGYAFENFDFNPIFEIPVIRIGDMQKEKILY 62

Query: 64  LPKDGNSRQSDTSTVSIF--AKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
              D   +  +   +  F  +   IL    G    K    D D        V   +  L 
Sbjct: 63  ---DNCLKTKEKEKLKQFLISNNDILIALSGATTGKIAFCDTDNKAYINQRVAIVRSKL- 118

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           +L++ + L+   +  IE  C G+   +   K IG   +P+PPL EQ  I   +  +  +I
Sbjct: 119 KLVKYYFLTRGFSLLIELACNGSAQPNISTKEIGEFKIPLPPLKEQEQIANFLDEKCEQI 178

Query: 182 DTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF---F 238
              I ++ + I LLKE+KQA ++  +TKGL+ ++  KDSGIEW+G +P HWEVK F   F
Sbjct: 179 ANFIEKKEKLISLLKEQKQAFINETITKGLDKNINFKDSGIEWLGEIPQHWEVKKFKMLF 238

Query: 239 ALVTELNRKNTKLIESNILSLSYGNIIQKLETR---NMGLKPESYETYQIVDPGEIV--- 292
            L   LN      +   I  +SYG I  K   R    +   P   +TY    P  ++   
Sbjct: 239 TLGNGLNITKADFVSYGIPCVSYGEIHSKYPCRLNTTIHTLPFVSKTYLADKPQSLLQKG 298

Query: 293 -FRFIDLQND-KRSLRSAQVMERGIITSAYMAV--KPHG-IDSTYLAWLMRSY------- 340
            F F D   D + S     +     I + Y  +  K  G I+S Y ++L  S        
Sbjct: 299 DFVFADTSEDIEGSGNFTSIQSDTPIFAGYHTIILKYKGKINSLYFSFLFDSIFTRNQIR 358

Query: 341 -DLC--KVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQ 375
            ++C  KVF    S L         K +  L+PP+KEQ
Sbjct: 359 KEVCGVKVFSITKSIL---------KEVQCLIPPLKEQ 387



 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/215 (25%), Positives = 100/215 (46%), Gaps = 20/215 (9%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESN----ILSLSYGNI-IQKLETR 271
            K+SGIEW+G +P+HWEV     +VT +N    +  + N    I  +  G++  +K+   
Sbjct: 4   FKESGIEWLGEIPEHWEVVKINKIVTFVNGYAFENFDFNPIFEIPVIRIGDMQKEKILYD 63

Query: 272 NMGLKPESYETYQ-IVDPGEIVFRFIDLQNDKRSL----RSAQVMER-GIITSAYMAVKP 325
           N     E  +  Q ++   +I+         K +       A + +R  I+ S    VK 
Sbjct: 64  NCLKTKEKEKLKQFLISNNDILIALSGATTGKIAFCDTDNKAYINQRVAIVRSKLKLVKY 123

Query: 326 HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
           +        +L R + L       GS  + ++  +++    + +PP+KEQ  I N ++ +
Sbjct: 124 Y--------FLTRGFSLLIELACNGSA-QPNISTKEIGEFKIPLPPLKEQEQIANFLDEK 174

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
             +I   +EK E+ I LLKE++ +FI   +T  +D
Sbjct: 175 CEQIANFIEKKEKLISLLKEQKQAFINETITKGLD 209


>gi|229163473|ref|ZP_04291424.1| hypothetical protein bcere0009_42390 [Bacillus cereus R309803]
 gi|228620042|gb|EEK76917.1| hypothetical protein bcere0009_42390 [Bacillus cereus R309803]
          Length = 441

 Score =  127 bits (320), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 116/439 (26%), Positives = 205/439 (46%), Gaps = 31/439 (7%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           YK Y  YK S VQWIG +PKHW+   +K+ + +   R +E   D  +  L   + G  K 
Sbjct: 3   YKPYEHYKSSDVQWIGKVPKHWE---LKKISSIFEQR-NEKVSDKDFEPLSVTKMGILKQ 58

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK------ 117
           L     +  +D     +  K   +            ++ FDG  S    V++PK      
Sbjct: 59  LENVAKTDNNDNRKKVL--KNDFVINSRSDRKGSCGVSKFDGSVSLICTVIKPKTINTYM 116

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
           D    L +  + S +  +    I +   +    W     I +PIPP  EQ  I   +   
Sbjct: 117 DYYHHLFRNKMFSEEFYRWGRGIVDD--LWSTKWDEFKRILIPIPPHEEQKSIVSYLNHI 174

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK-- 235
              I+ LIT + + IE +++ +++L++  VT GLNP  KMKDS +EW+G +P+HW  K  
Sbjct: 175 YEAIEELITHKQQQIETIQQYQRSLITEAVTSGLNPHAKMKDSSVEWIGEMPEHWITKRL 234

Query: 236 PFFALV-TELNRKN---TKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEI 291
            F ++V   L  K    ++  E+  + L+  N I+K +     +   S + Y+  +  EI
Sbjct: 235 DFVSVVKARLGWKGLTASEYQENGYIFLAIPN-IKKFQIDFENVNYISEKRYK--ESPEI 291

Query: 292 VFRFID--LQNDKRSLRSAQVMER----GIITSAYMAVKPHG-IDSTYLAWLMRSYDLCK 344
           + +  D  L  D  +L    V+        + S+   ++P G + S +L + ++S  + K
Sbjct: 292 MLQVGDVLLAKDGSTLGEVNVVRYLPSPATVNSSIAVIRPKGDLHSVFLYYYLKSNYIQK 351

Query: 345 VFYAMGSGLRQSLKFE-DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
           +      G+     F+ D+ +  + VPP+ EQ  I   ++ + + I+ L+ + ++ I +L
Sbjct: 352 IIQKKKDGMGVPHLFQKDINKFIIQVPPLDEQVKIAKYLDGKISEINNLIIETQEQIDIL 411

Query: 404 KERRSSFIAAAVTGQIDLR 422
           ++ R S +   VTG+ID+R
Sbjct: 412 QQYRQSLVYEVVTGKIDVR 430


>gi|78356903|ref|YP_388352.1| type I restriction enzyme, S subunit [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
 gi|78219308|gb|ABB38657.1| type I restriction enzyme, S subunit [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 474

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 111/447 (24%), Positives = 199/447 (44%), Gaps = 32/447 (7%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYI----GLEDV 56
           M     YP+YKD+GV W+G+IP HW     K + K    R+    ++++ +    G+   
Sbjct: 1   MMKLAPYPEYKDAGVSWVGSIPAHWPEKRAKYYFKEIDDRSQTGDEEMLSVSHITGVTPR 60

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
                     + N  Q           G ++   +  ++    +++  GI S  + V +P
Sbjct: 61  SQKNVTMFKAESNVGQKRCQP------GDLIINTMWAWMSALGVSNHAGIVSPAYGVYRP 114

Query: 117 K---DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWK----GIGNIPMPIPPLAEQVL 169
           +   D     L   LL I+   R E IC    +  +  +       ++P+  PP  EQ  
Sbjct: 115 RSNQDYDYYYLDS-LLRIE-GYRSEYICRSTGIRSSRLRLYPDKFLSMPVVCPPQEEQQT 172

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   + A+       I  + RFIELLKE+KQ +++  VT+GL+P V+ K SG+EW+G +P
Sbjct: 173 IARFLKAQDRLFRKFIRNKRRFIELLKEQKQNVINQAVTRGLDPKVQFKPSGVEWIGDIP 232

Query: 230 DHWEVKPFFALVTELNR---KNTKLIESNILSLSYGNIIQK------LETRNMGLKPESY 280
           +HW+ +    L         KNT   E  ++  +Y ++ +       ++       PE  
Sbjct: 233 EHWDARRLRTLAAVRASGVDKNTNEDEVPVMLCNYVDVYKNDRITAAIDFMKATATPEEI 292

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA-VKPHG--IDSTYLAWLM 337
             +++     I+ +  +  +D            G++ + ++A ++P    I+  +L    
Sbjct: 293 RAFELKAGDVIITKDSESWDDIAIPTFVPETIPGVVCAYHLALIRPFSGEIEGEFLFRAF 352

Query: 338 RSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
            S  +   F    +G+ R  L    +K     +PP++EQ  I   IN + A I   + + 
Sbjct: 353 SSDPVADQFRIAATGVTRFGLAQGAIKGAFFPLPPLEEQRAIIAHINEKCAEISQAISRA 412

Query: 397 EQSIVLLKERRSSFIAAAVTGQIDLRG 423
           E+ I L++E R+  I+  VTGQ+D+RG
Sbjct: 413 EREIELMREYRTRLISDVVTGQVDVRG 439


>gi|114047283|ref|YP_737833.1| restriction modification system DNA specificity subunit [Shewanella
           sp. MR-7]
 gi|113888725|gb|ABI42776.1| restriction modification system DNA specificity domain [Shewanella
           sp. MR-7]
          Length = 448

 Score =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 116/441 (26%), Positives = 208/441 (47%), Gaps = 54/441 (12%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY--- 63
           Y  YKDSGV+W+G IP++WKV+  K    + TG     GK+      ED ++GTGKY   
Sbjct: 35  YEAYKDSGVEWLGDIPQNWKVMRFKFLASITTG-----GKNT-----ED-KTGTGKYPFF 83

Query: 64  ----LPKDGNSRQSDTSTVSIFAKG-------QILYGKLGPYLRKAIIADFDGICSTQFL 112
               +P+  +S   D   +     G         + GK   + R    +DF+ +      
Sbjct: 84  VRSQIPEKIDSYSYDGEAILTAGDGAGVGKVYHYINGKFDFHQRVYKFSDFNEVIGQYLF 143

Query: 113 VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHAD-WKGIGNIPMPIPPLAEQVLIR 171
                +     + G   S   + R+  I +      +D W              +Q LI 
Sbjct: 144 HYLYVNFFNVAVLGTAKSTVDSLRLPLIQDFQVCYPSDNW--------------QQQLIV 189

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
             I  +  +ID  I  + + I LLKE+KQ ++   VT+GL+P+V MKDSG++W+G +P H
Sbjct: 190 SYINKKAAQIDDAIAIKEQQISLLKERKQIIIQQAVTQGLDPNVPMKDSGVDWIGKIPAH 249

Query: 232 WEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPGE 290
           WEV+    +  E++ + +K  +  +LS+S+   +     +N+ +   E Y   ++    +
Sbjct: 250 WEVRRAKYIFDEIDER-SKNGDEELLSVSHMTGVTPRSEKNVSMFMAEDYTGSKLCIEND 308

Query: 291 IVFRFIDLQNDKRSLRSAQVMER-GIITSAYMAVK---PHGIDSTYLAWLMRSYDLCKVF 346
           +V   +        + +  V +R GI++ +Y   +    +  + TYL +L++S    + +
Sbjct: 309 LVINIM-----WAWMGALGVSDRVGIVSPSYGVFRQKLKNTFNPTYLEYLLKSVKYVEYY 363

Query: 347 YAMGSGLRQS-LKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
             + +GL  S L+F    +  + +  P  +EQ +I   ++ +T RID+ ++     I  L
Sbjct: 364 NKVSTGLHSSRLRFYGHMLFAMKMGYPSYEEQNEIMAYLHEQTKRIDLAIDSQLAQIEKL 423

Query: 404 KERRSSFIAAAVTGQIDLRGE 424
           KE +++ I +AVTG+I +  E
Sbjct: 424 KEYKTTLINSAVTGKIKITPE 444


>gi|239828721|ref|YP_002951344.1| restriction modification system DNA specificity domain protein
           [Geobacillus sp. WCH70]
 gi|239809014|gb|ACS26078.1| restriction modification system DNA specificity domain protein
           [Geobacillus sp. WCH70]
          Length = 445

 Score =  126 bits (317), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 119/441 (26%), Positives = 199/441 (45%), Gaps = 38/441 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKD--G 68
           KDSGV+WIG IP  WK++ +K   K    + S    + I + L  +E G   Y  K   G
Sbjct: 6   KDSGVEWIGEIPSDWKILRLKNVLKERNEKNSPIKTNEI-LSLT-IEKGVIPYKEKKSGG 63

Query: 69  NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPEL-LQGW 127
           N  + D S   +     I+   +   +    I+ + G  S  + VL   DV   +    +
Sbjct: 64  NKAKEDLSNYKLAYPNDIVLNSMNVIVGAVGISKYYGCVSPVYYVLYSDDVEQNIRFYNY 123

Query: 128 LLSIDVTQR-IEAICEGATMSHADWKGIG------------NIPMPIPPLAEQVLIREKI 174
           L      Q+ +  +  G  M  +    +             N+ +P+PP++ Q  I   +
Sbjct: 124 LFQSSAFQKSLIGLGNGIMMKQSSTGKLNTIRLRIPLDRLKNVYLPVPPVSVQQKIVNFL 183

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             +   IDT+I +  + IE LK+ KQ+L++  VTKGL+P+V+MKDSGIEWVG +P HWE+
Sbjct: 184 DEKVSHIDTIIEKNKQSIEELKKYKQSLIAETVTKGLDPNVEMKDSGIEWVGEIPKHWEI 243

Query: 235 KPF--FALVTELNRKNTKLIESN---ILSLSYGNIIQKLETR-------NMGLKPESYET 282
           +     +++T      +K  E N   +  + Y N+  K E +        + +    Y+ 
Sbjct: 244 RRLRDISIITRGTVDKSK--EKNEIPVYLVQYTNVYYKREQKINDDDYLPITVSENEYKK 301

Query: 283 YQIVDPGEIVFRFIDLQNDK--RSLRSAQVMERGIITSAYMAVK-PHGI-DSTYLAWLMR 338
           Y+ V  G+I+        D    S    + +   +  S  + ++ P+ I D  Y  + M 
Sbjct: 302 YK-VRKGDILLTASSETKDDIGHSTVIVEDLPNHVFGSDIIRIRIPNKIVDLNYKKYFME 360

Query: 339 SYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           +Y     F  +  G+ R     +  K L  ++PPI+EQ  I   ++  T  I+ L+   E
Sbjct: 361 NYYYLAKFDKLSRGITRFRFGMDQFKSLKYVIPPIEEQVKIAKYLDNITNHINQLICNKE 420

Query: 398 QSIVLLKERRSSFIAAAVTGQ 418
           + I  L+  + S I   VTG+
Sbjct: 421 KLINELESYKKSLIYEYVTGK 441



 Score = 77.0 bits (188), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 59/224 (26%), Positives = 109/224 (48%), Gaps = 25/224 (11%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSY-GNIIQKLETRNMG 274
           KMKDSG+EW+G +P  W++     ++ E N KN+ +  + ILSL+    +I   E ++ G
Sbjct: 4   KMKDSGVEWIGEIPSDWKILRLKNVLKERNEKNSPIKTNEILSLTIEKGVIPYKEKKSGG 63

Query: 275 LKP-ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER--GIITSAYMAVKPHGIDST 331
            K  E    Y++  P +IV   +++      +  A  + +  G ++  Y  +    ++  
Sbjct: 64  NKAKEDLSNYKLAYPNDIVLNSMNV------IVGAVGISKYYGCVSPVYYVLYSDDVEQN 117

Query: 332 --YLAWLMRSYDLCKVFYAMGSG-------------LRQSLKFEDVKRLPVLVPPIKEQF 376
             +  +L +S    K    +G+G             +R  +  + +K + + VPP+  Q 
Sbjct: 118 IRFYNYLFQSSAFQKSLIGLGNGIMMKQSSTGKLNTIRLRIPLDRLKNVYLPVPPVSVQQ 177

Query: 377 DITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            I N ++ + + ID ++EK +QSI  LK+ + S IA  VT  +D
Sbjct: 178 KIVNFLDEKVSHIDTIIEKNKQSIEELKKYKQSLIAETVTKGLD 221


>gi|150005916|ref|YP_001300660.1| type I restriction-modification system S subunit [Bacteroides
           vulgatus ATCC 8482]
 gi|149934340|gb|ABR41038.1| type I restriction-modification system S subunit [Bacteroides
           vulgatus ATCC 8482]
          Length = 430

 Score =  125 bits (315), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 75/205 (36%), Positives = 117/205 (57%), Gaps = 3/205 (1%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI-IQKLETRNMGLK 276
           KDSGI+W+G +P HWE+K    +  E    N+    +N L   +G I  +K +  +  LK
Sbjct: 8   KDSGIQWLGKIPSHWEIKRSRLIFDENVETNSTCNNTNQLQFRFGTIEPKKSQEMDSDLK 67

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAW 335
            +    Y IV  G+I+   ++L  D  S R AQV E+GIITSAY+A++P   I S Y  +
Sbjct: 68  -KIISKYTIVQNGDIMINGLNLNYDFVSQRVAQVKEKGIITSAYIALRPKENICSDYFTY 126

Query: 336 LMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           L++  D  KVF+ MG G+R +L F++ +   + +PP++EQ  +   ++  TA ID  + +
Sbjct: 127 LLKGMDARKVFHGMGCGVRLTLSFKEFRNELLPIPPLEEQQSMATYLDKATAEIDKAIAQ 186

Query: 396 IEQSIVLLKERRSSFIAAAVTGQID 420
            ++ I LL ER+   I  AVT  +D
Sbjct: 187 QQRMIDLLNERKQIIIQRAVTKGLD 211



 Score =  124 bits (311), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 115/464 (24%), Positives = 193/464 (41%), Gaps = 87/464 (18%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y  YKDSG+QW+G IP HW++   +     N    S             ++   G   PK
Sbjct: 4   YNSYKDSGIQWLGKIPSHWEIKRSRLIFDENVETNSTCN------NTNQLQFRFGTIEPK 57

Query: 67  DGNSRQSD----TSTVSIFAKGQILYGKLGPYL-----RKAIIADFDGICSTQFLVLQPK 117
                 SD     S  +I   G I+   L         R A + +  GI ++ ++ L+PK
Sbjct: 58  KSQEMDSDLKKIISKYTIVQNGDIMINGLNLNYDFVSQRVAQVKE-KGIITSAYIALRPK 116

Query: 118 -DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
            ++  +     L  +D  +    +  G  ++ + +K   N  +PIPPL EQ  +   +  
Sbjct: 117 ENICSDYFTYLLKGMDARKVFHGMGCGVRLTLS-FKEFRNELLPIPPLEEQQSMATYLDK 175

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
            T  ID  I ++ R I+LL E+KQ ++   VTKGL+ +V+MK+SG+ W+G +P HWE  P
Sbjct: 176 ATAEIDKAIAQQQRMIDLLNERKQIIIQRAVTKGLDGNVEMKNSGLNWLGQIPSHWESLP 235

Query: 237 FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFI 296
                                 L+Y       E RN G  P   +     +     +R  
Sbjct: 236 ----------------------LTY-----VFEMRN-GYTPSKNDPTYWTNGSIPWYRME 267

Query: 297 DLQNDKRSLR---------------------------SAQVMERGIITSAYMA------- 322
           D++   R LR                           +A + E  ++ +  +A       
Sbjct: 268 DIRKSGRFLREAMQYVTTKAINGKGTFKAGSYIMAICTASIGEHAMLIADSLANQRFANF 327

Query: 323 -VKPHGIDSTYLAWLMRSY----DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFD 377
            ++   I+S Y  +L        D C+      S   Q +    +KR P+  P ++EQ +
Sbjct: 328 KIRKSLIESFYPLFLFYYMYVVGDFCRE--NSNSTCFQYVDMGALKRFPIPKPSMEEQKN 385

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           I + +     +I+  +E+I++ I LL+ER+   I+  VTG+I +
Sbjct: 386 IVSSLTQNLQQINTALERIQKQITLLQERKQIIISEVVTGKIKV 429


>gi|322420420|ref|YP_004199643.1| restriction modification system DNA specificity domain-containing
           protein [Geobacter sp. M18]
 gi|320126807|gb|ADW14367.1| restriction modification system DNA specificity domain protein
           [Geobacter sp. M18]
          Length = 459

 Score =  125 bits (315), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 110/440 (25%), Positives = 194/440 (44%), Gaps = 33/440 (7%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYI----GLEDV 56
           M     YP Y+D+GV W+G+IP HW     K + K    R+    ++++ +    G+   
Sbjct: 1   MMKLAPYPDYRDAGVSWVGSIPAHWPEKRAKYYFKEIDERSQTGDEEMLSVSHITGVTPR 60

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
                     + N  Q           G ++   +  ++    +++  GI S  + V +P
Sbjct: 61  SQKNVTMFKAESNVGQKRCQP------GDLVINTMWAWMSALGVSNHAGIVSPAYGVYRP 114

Query: 117 KD--VLPELLQGWLLSIDVTQRIEAICEGATMSHADWK----GIGNIPMPIPPLAEQVLI 170
           +            LL I+   R E IC    +  +  +       ++P+  PP  EQ  I
Sbjct: 115 RSNQAYDNYYLDHLLRIE-GYRSEYICRSTGIRSSRLRLYPDKFLSMPVVCPPQEEQQTI 173

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              + A+       I  + R IELLKE+KQ +++  VT+GL+P VK K SG+EW+G +P+
Sbjct: 174 ARFLKAQDRLFRKFIRNKRRLIELLKEQKQNVINQAVTRGLDPKVKFKPSGVEWIGDIPE 233

Query: 231 HWEVKPFFALVTELNRKNT-KLIESNILSLSYGNIIQKLETRNMGLKPESYETYQI--VD 287
           HWEV+    L   LN + + K      ++L +   ++    R      E     Q+    
Sbjct: 234 HWEVRRLKFLCHNLNEQTSEKQPGETYIALEH---VESWTGRISLPDDEISFDSQVKRFK 290

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVF 346
           PG+++F    L+     +   Q    G+    ++ ++  G + + +L   +RS  +  + 
Sbjct: 291 PGDVLFG--KLRPYLAKVTRPQTA--GVCVGEFLVLRATGNVSANFLEQKLRSKRVIDLI 346

Query: 347 YAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
            +   G    R    F  +  L    PP  EQ +I   I  ++A ID  + + ++ I L+
Sbjct: 347 NSSTFGAKMPRADWTF--IGNLKFTYPPADEQQEILEHIQEKSAEIDQAISRAQREIELM 404

Query: 404 KERRSSFIAAAVTGQIDLRG 423
           +E R+  I+  VTGQ+D+RG
Sbjct: 405 REYRTRLISDVVTGQVDVRG 424


>gi|259156571|gb|ACV96514.1| restriction modification system DNA specificity domain [Vibrio
           fluvialis Ind1]
          Length = 389

 Score =  125 bits (315), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 101/386 (26%), Positives = 181/386 (46%), Gaps = 31/386 (8%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGKYLP 65
           Y  YK+SG  WIG IP  W++VPI+   K    + S    ++I+ +    + +G  KY  
Sbjct: 10  YEVYKNSGEDWIGDIPSGWELVPIRSIFKFRNEKNSPVKTEEILSL---SIANGVTKYSD 66

Query: 66  KD--GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL--QPKDVLP 121
           K   GN R+ D S   I     I+   +   +    ++ + G  S  +  L  + +DVL 
Sbjct: 67  KGRGGNKRKDDISAYKIAHPKDIVLNSMNVIVGAVGMSKYHGAISPVYYALYTESEDVLV 126

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPM------------PIPPLAEQVL 169
           E  +   L+    + +    +G  +  +    +  I M            P PP+AEQ L
Sbjct: 127 EYYEKIFLNEGFQRGLLKFGKGILIKLSGTGKLNTIRMKVSTDDLKSLYFPKPPIAEQNL 186

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  +T +ID  I+ + + I LLKE+ Q ++   VT+GLN +V MKD+GI+W+G +P
Sbjct: 187 IFSFLDKKTAQIDEAISIKEQQINLLKERNQIIIHKAVTQGLNSNVLMKDTGIDWIGKIP 246

Query: 230 DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPG 289
           +HW++     ++ +LNR   K  ++ I S ++G   + L   N GL   +   YQ VD G
Sbjct: 247 EHWDISLAKHILKKLNRPRKKNGDTVICS-NHG-CSKLLGEVNQGLVSLTQHDYQGVDEG 304

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAM 349
           +++   +D  +   ++        G  TS       H  +  Y+A+ ++   +  V+  +
Sbjct: 305 DLLVHGMDAWHGAIAISE----HTGDCTSVVHVCDSH-FNKVYIAYFLKMLAIMNVYKVI 359

Query: 350 GSGLRQSL----KFEDVKRLPVLVPP 371
            +G+R +      +     + +++PP
Sbjct: 360 SNGVRGNTSDFRSWSKFGEIQIILPP 385



 Score = 70.9 bits (172), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 94/229 (41%), Gaps = 47/229 (20%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMG--L 275
           K+SG +W+G +P  WE+ P  ++    N KN+ +    ILSLS  N + K   +  G   
Sbjct: 14  KNSGEDWIGDIPSGWELVPIRSIFKFRNEKNSPVKTEEILSLSIANGVTKYSDKGRGGNK 73

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLA 334
           + +    Y+I  P +IV   ++                 +I  A    K HG I   Y A
Sbjct: 74  RKDDISAYKIAHPKDIVLNSMN-----------------VIVGAVGMSKYHGAISPVYYA 116

Query: 335 WLMRSYDLCKVFY--------------AMGSGL-------------RQSLKFEDVKRLPV 367
               S D+   +Y                G G+             R  +  +D+K L  
Sbjct: 117 LYTESEDVLVEYYEKIFLNEGFQRGLLKFGKGILIKLSGTGKLNTIRMKVSTDDLKSLYF 176

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
             PPI EQ  I + ++ +TA+ID  +   EQ I LLKER    I  AVT
Sbjct: 177 PKPPIAEQNLIFSFLDKKTAQIDEAISIKEQQINLLKERNQIIIHKAVT 225


>gi|163788850|ref|ZP_02183295.1| hypothetical protein FBALC1_11452 [Flavobacteriales bacterium
           ALC-1]
 gi|159876087|gb|EDP70146.1| hypothetical protein FBALC1_11452 [Flavobacteriales bacterium
           ALC-1]
          Length = 440

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 124/441 (28%), Positives = 201/441 (45%), Gaps = 45/441 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           MK+  +Y     S + W+  IP HWK V +   +  N  +   S KD  +  L   ++G 
Sbjct: 1   MKNNHSY--LNTSKIDWLNKIPNHWKEVRLG--SVFNERKEKVSDKD--FPPLSVTKNGI 54

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
              L     S   D   + +   G             + ++ +DG  S   +VL+P D++
Sbjct: 55  VPQLENAAKSNDGDNRKLVL--SGDFAINSRSDRKGSSGLSIYDGSVSLINIVLKPIDII 112

Query: 121 P----ELLQGWLLSIDVTQRIEAICEGA-TMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           P     LL+ +    +  +    I E   T  +++ K   N+ +P+PP  EQ  I   + 
Sbjct: 113 PVFSQYLLKSYFFKEEYYRYGRGIVEDLWTTRYSEMK---NMIIPLPPKQEQTTIANFLD 169

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            +T +I+  IT++ + IELL E+K A+++  V KG+NP+V MKDSGIEW+G +P+HWEV+
Sbjct: 170 YKTEKINRFITKKKQLIELLNEQKAAIINQAVIKGINPNVPMKDSGIEWLGEIPEHWEVR 229

Query: 236 PF-----FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETY-QIVDPG 289
                    + TE N K     ES    ++  NI  K   R + L   S+E    I   G
Sbjct: 230 KLKYSVRLNMHTEFNNK-----ESIKNKIALENIEGKT-GRILALNENSFEGVGTIFKKG 283

Query: 290 EIVFRFIDLQNDKRSLRSAQVME---RGIITSAYMAVKPHGID--STYLAWLMRSYDLCK 344
           +++F        K     A+V+     G   +  + + P+  D    YL + M + D   
Sbjct: 284 DVLF-------GKLRPYLAKVVSPNFEGSCVNELLVLTPNRNDWNPKYLKYRMLASDFIS 336

Query: 345 VFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
           +      G    R S  F  +  L +  P   EQ +I   I  ET  +   +  I + I 
Sbjct: 337 IVDNSTYGAKMPRASWNF--IGTLKISKPNKTEQSEIVRFIEKETELVSKTIITIAKEIS 394

Query: 402 LLKERRSSFIAAAVTGQIDLR 422
           L++E +++ IA AVTG+ID+R
Sbjct: 395 LVEEYKTALIADAVTGKIDVR 415


>gi|167771153|ref|ZP_02443206.1| hypothetical protein ANACOL_02508 [Anaerotruncus colihominis DSM
           17241]
 gi|167666823|gb|EDS10953.1| hypothetical protein ANACOL_02508 [Anaerotruncus colihominis DSM
           17241]
          Length = 444

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 103/334 (30%), Positives = 170/334 (50%), Gaps = 21/334 (6%)

Query: 101 ADFDGICSTQFLVLQPKD-VLP---ELLQGWLLSIDVTQR-IEAICEGATMSHADWKGIG 155
           A + GI S  + ++ PK  ++P     L    L I++ Q  +  I EG  +   D+  + 
Sbjct: 95  AYYQGIISPAYTIMVPKQKIVPGYFRYLAKSRLFIELLQLCVTGIREGQNI---DYGKLK 151

Query: 156 NIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDV 215
           N  +P+PP  EQ  I   +  +T +++ LI  + R I LL+E++QA ++Y+VT+GL+ + 
Sbjct: 152 NHLIPVPPSEEQDQIVRYLDWQTSKVNRLINAKKRIISLLEEQQQATIAYVVTRGLDQNA 211

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET-RNMG 274
           ++ DSGI+++G VP HW+V     +  E +RK  +  E  +LSLS  + +   E  +   
Sbjct: 212 ELMDSGIDYIGKVPAHWKVLLNHRIYKEKSRKFGE--EETVLSLSQKDGLLPYENMKERS 269

Query: 275 LKPESYETYQIVDPGEIVF-RFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTY 332
           L   SYE +++V P ++V  RF   +       S+    RGI+T  Y   +P   I S Y
Sbjct: 270 LHTASYENWKLVFPNDLVLNRF---KAHLGVFFSSNY--RGIVTFHYGVYEPVMKISSKY 324

Query: 333 LAWLMRSYDLCKVFYAMGSGLR---QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
              L  + +  +VF +  +G+    Q+L   +   +  + PP +EQ  I   I     + 
Sbjct: 325 YEALYHTPEFRRVFASKSNGMTVGLQNLSNTNFYSVYTVYPPHEEQCQIVCKIKEIEEKY 384

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
             L+ KI Q I  L E R+  I+  VTGQID+R 
Sbjct: 385 RDLIAKINQEIDCLHEYRTRLISDVVTGQIDVRN 418



 Score = 50.8 bits (120), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 51/214 (23%), Positives = 100/214 (46%), Gaps = 28/214 (13%)

Query: 224 WVGLVPDHWE---VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY 280
           W+  +PD WE   +K  F+  +E    +  L+               + ++NMG+ P+  
Sbjct: 14  WLTQIPDSWEDIKIKFLFSERSEKGYPDEPLL---------------VASQNMGVVPKGV 58

Query: 281 ETYQIVDPGE--IVFRFIDLQNDKRSLRSAQ-----VMERGIITSAYMAVKP-HGIDSTY 332
              + V   +   + + + + +   SLRS Q        +GII+ AY  + P   I   Y
Sbjct: 59  YGNRTVQATKDLHLLKLVRVGDFVISLRSFQGGIEYAYYQGIISPAYTIMVPKQKIVPGY 118

Query: 333 LAWLMRSYDLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
             +L +S    ++     +G+R  Q++ +  +K   + VPP +EQ  I   ++ +T++++
Sbjct: 119 FRYLAKSRLFIELLQLCVTGIREGQNIDYGKLKNHLIPVPPSEEQDQIVRYLDWQTSKVN 178

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
            L+   ++ I LL+E++ + IA  VT  +D   E
Sbjct: 179 RLINAKKRIISLLEEQQQATIAYVVTRGLDQNAE 212


>gi|126664066|ref|ZP_01735060.1| type I restriction-modification system, S subunit [Flavobacteria
           bacterium BAL38]
 gi|126624015|gb|EAZ94709.1| type I restriction-modification system, S subunit [Flavobacteria
           bacterium BAL38]
          Length = 450

 Score =  125 bits (313), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 123/455 (27%), Positives = 209/455 (45%), Gaps = 51/455 (11%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K+YP+YK S + W   IP++W    +K       G T  +  D  +       +G   +L
Sbjct: 2   KSYPKYKPSKIVWYPEIPENWDYCKVKHIANTYAGGTPSTVVDSFW------HNGDIPWL 55

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLR--KAIIADFDGICST-QFLVLQPK---- 117
           P  G  +  +  +   F   + L G    +++    ++A     C+   +L  Q      
Sbjct: 56  PS-GKLQNCEIISAEKFITNEGLIGSSTKWIKPNTVLVALTGATCANIGYLTFQACANQS 114

Query: 118 ----DVLPELLQG---WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
               D  PE       + + +++  +I     G   +  +   + N+ +  P L EQ+ I
Sbjct: 115 VIAVDENPEKANSRFLYYMFLNMRSQILTHQTGGAQAGINDSDVKNLYLLNPSLEEQIKI 174

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
            + +  +T  ID  I ++ R IELLKEK+QA+++  VTKGLNP+  MKDSG+EW+G +P+
Sbjct: 175 ADYLDYKTNLIDATIEKKKRLIELLKEKRQAVINEAVTKGLNPNAPMKDSGLEWLGEIPE 234

Query: 231 HWEVKPFFALVTELNR----------KNTKLIESNILSLSYGNIIQ-KLETRNMGLKPES 279
           +WEVK    L++  N           K   L ++ I     GN+I+      +  + PE 
Sbjct: 235 NWEVKKVKYLLSSENGIKIGPFGSALKLDTLTDNGIKIYGQGNVIKDDFTLGHRYIDPER 294

Query: 280 YE----TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG--IDSTYL 333
           +E     Y+I+D G+I+   +      +   S+   E+GI+ S  + ++ +    D    
Sbjct: 295 FEKDFKQYEILD-GDILITMMGTTGKSKVFNSS--YEKGILDSHLLRLRFNEDLFDGRLF 351

Query: 334 AWLMRSYDLCKVFYAMGS------GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETA 387
           + L+   D      A+ S      GL  S+    VK L ++ P ++ Q +I N I+    
Sbjct: 352 SILLEQSDYVFQQLALNSVGSIMAGLNSSI----VKELIIITPKLEIQKEILNYIDENCK 407

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            ID++  KI   I  L+  R S I+ AVTG+ID+R
Sbjct: 408 IIDIISSKILSQIEKLQTYRQSLISEAVTGKIDVR 442


>gi|74318700|ref|YP_316440.1| putative restriction endonuclease S subunit [Thiobacillus
           denitrificans ATCC 25259]
 gi|74058195|gb|AAZ98635.1| putative restriction endonuclease S subunit [Thiobacillus
           denitrificans ATCC 25259]
          Length = 400

 Score =  125 bits (313), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 108/410 (26%), Positives = 183/410 (44%), Gaps = 30/410 (7%)

Query: 20  AIPKHWKVVPIKRFTKLNTGRT--SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           + P  W+ + +K    L +G     ES K+            TG Y    GN  +  T++
Sbjct: 7   SAPISWRRMKLKYLVALKSGEAIPGESIKE------------TGDYPVYGGNGFRGYTNS 54

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRI 137
            +   + +IL G+ G        A+     +   +V  PK         WL        +
Sbjct: 55  FTHEGE-RILIGRQGALCGNINYAEGKFWATEHAIVATPKT---NFETAWLGETLRVMNL 110

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKE 197
               + A       + + N+ + +PP  EQ  I + +   +  ID LI E+ + + LL E
Sbjct: 111 NQYSQSAAQPGIAVEVVENLVIAVPPEGEQRRIADSLHQLSAPIDKLILEKQKLLTLLTE 170

Query: 198 KKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNIL 257
           K++ +++  + KGLN D   +DS I W+G +P HW+V+    L TE + ++    E  + 
Sbjct: 171 KRRTVIADFLIKGLNKDTPRRDSDIPWLGEIPAHWKVERAKWLFTERDDRSDSGDEELLT 230

Query: 258 SLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER--GI 315
                 +  + E        ES E Y+  + G++V       N   +   A  + R  GI
Sbjct: 231 VSHLTGVTSRAEKDVNMFMAESLEGYKRCEAGDLVI------NTLWAWMGAMGIARQPGI 284

Query: 316 ITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPP 371
           ++ AY   +P   +D  Y+  L+R+    +       G+   R  L  E +    + VPP
Sbjct: 285 VSPAYNVYQPVAQLDPEYIDLLVRTPRFVEEITRYSKGVWSSRLRLYPEGLYEAWLPVPP 344

Query: 372 IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           + EQ DI   +  ET ++D L E  E+++ +L+ERRS+ I+AAVTGQ+DL
Sbjct: 345 LDEQRDIVARVQAETRKLDALAEATERTVTVLQERRSALISAAVTGQLDL 394



 Score = 61.2 bits (147), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 92/206 (44%), Gaps = 7/206 (3%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           +DS + W+G IP HWKV   K        R+    ++++ +      +G      KD N 
Sbjct: 191 RDSDIPWLGEIPAHWKVERAKWLFTERDDRSDSGDEELLTVSH---LTGVTSRAEKDVNM 247

Query: 71  RQSDT-STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL-PELLQGWL 128
             +++         G ++   L  ++    IA   GI S  + V QP   L PE +   +
Sbjct: 248 FMAESLEGYKRCEAGDLVINTLWAWMGAMGIARQPGIVSPAYNVYQPVAQLDPEYIDLLV 307

Query: 129 LSIDVTQRIEAICEGATMSHADW--KGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
            +    + I    +G   S      +G+    +P+PPL EQ  I  ++ AET ++D L  
Sbjct: 308 RTPRFVEEITRYSKGVWSSRLRLYPEGLYEAWLPVPPLDEQRDIVARVQAETRKLDALAE 367

Query: 187 ERIRFIELLKEKKQALVSYIVTKGLN 212
              R + +L+E++ AL+S  VT  L+
Sbjct: 368 ATERTVTVLQERRSALISAAVTGQLD 393


>gi|289166196|ref|YP_003456334.1| type I restriction-modification system (methylase_S) [Legionella
           longbeachae NSW150]
 gi|288859369|emb|CBJ13305.1| putative type I restriction-modification system (methylase_S)
           [Legionella longbeachae NSW150]
          Length = 466

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 114/441 (25%), Positives = 207/441 (46%), Gaps = 33/441 (7%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K Y  YK+S  +W+  IP+HW     K   K+   R+ +  ++++      V    G  L
Sbjct: 2   KPYSSYKNSSEKWLNKIPEHWNFKRAKSVFKIIDIRSQDGSEELL-----SVSEKQGVAL 56

Query: 65  PKDGNS---RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--- 118
            K+ N    + ++ +   +     ++   L  ++     +++ GI ST + V +  D   
Sbjct: 57  RKNTNVTMFQAANYAGYKLCWPQDLVINSLWAWMTGLGFSEYHGIISTAYSVFRIWDQEK 116

Query: 119 ----VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
                   LL+  + + +   R + I         D     ++P+ +PPL+EQ  I   +
Sbjct: 117 FNYKYGNYLLRSKIYNWEFRVRSKGIWRSRYQLSDD--SFLSMPLLLPPLSEQQQIAIYL 174

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             +T +I+  I  + + I LLKE+KQ +++  VTKG+NPDV MKDSG++W+G +P+HWE+
Sbjct: 175 DWKTTKINKFIKAKKKLIALLKEQKQNIINEAVTKGINPDVNMKDSGVDWLGEIPEHWEI 234

Query: 235 KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPE--SYETYQI------- 285
           +    + T+     T    + +   S    ++       G+K E  +Y +  +       
Sbjct: 235 RKLKYVATKFGSGVTPKGGATVYQDSGIPFLRSQNIHFEGIKLENVAYISNDVHKRMSSS 294

Query: 286 -VDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP--HGIDSTYLAWLMRSYDL 342
            V P +++   I   +  R+      +E+  +      ++P    + S YLA+ + S  L
Sbjct: 295 HVKPNDVLLN-ITGASIGRTCYVPSNLEQANVNQHVCIIRPIQKKVSSQYLAFYL-SIPL 352

Query: 343 C--KVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
              K+        R+ L    +KRL V++P   EQ DI N I+ ET+ I+  ++K E  I
Sbjct: 353 IQRKILEEQNGASREGLTLSSIKRLNVILPTFNEQMDILNYISTETSVINKTIKKAELEI 412

Query: 401 VLLKERRSSFIAAAVTGQIDL 421
            L++E R+  I+  VTG+ID+
Sbjct: 413 ELIQEFRTRLISDVVTGKIDV 433



 Score = 37.4 bits (85), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 51/217 (23%), Positives = 102/217 (47%), Gaps = 12/217 (5%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           + P    K+S  +W+  +P+HW  K   ++   ++ ++    E  +LS+S    +   + 
Sbjct: 1   MKPYSSYKNSSEKWLNKIPEHWNFKRAKSVFKIIDIRSQDGSEE-LLSVSEKQGVALRKN 59

Query: 271 RNMGL-KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK---PH 326
            N+ + +  +Y  Y++  P ++V     L      L  ++    GII++AY   +     
Sbjct: 60  TNVTMFQAANYAGYKLCWPQDLVIN--SLWAWMTGLGFSEY--HGIISTAYSVFRIWDQE 115

Query: 327 GIDSTYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
             +  Y  +L+RS      F     G+   R  L  +    +P+L+PP+ EQ  I   ++
Sbjct: 116 KFNYKYGNYLLRSKIYNWEFRVRSKGIWRSRYQLSDDSFLSMPLLLPPLSEQQQIAIYLD 175

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            +T +I+  ++  ++ I LLKE++ + I  AVT  I+
Sbjct: 176 WKTTKINKFIKAKKKLIALLKEQKQNIINEAVTKGIN 212


>gi|302037229|ref|YP_003797551.1| putative type I restriction system, specificity protein HsdS
           [Candidatus Nitrospira defluvii]
 gi|300605293|emb|CBK41626.1| putative Type I restriction system, specificity protein HsdS
           [Candidatus Nitrospira defluvii]
          Length = 452

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 118/430 (27%), Positives = 183/430 (42%), Gaps = 42/430 (9%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           YP YKDSGV W+G +P  W    I R   L   R +E+G    ++ + +V   TG  +  
Sbjct: 8   YPAYKDSGVPWLGEVPLTWS---ISRNGGLFIQR-NETG--FAHLPILEVSLKTGVRVRN 61

Query: 67  -DGNSRQ---SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLP 121
            DG+ R+   SD        K  + Y  +  +     IA  DG+ S  ++V +P K V P
Sbjct: 62  LDGSGRKQIMSDRDKYKRARKDDLAYNMMRMWQGAIGIAPTDGLVSPAYVVARPLKGVEP 121

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHAD--WKGIGNIPMPIPPLAEQVLIREKIIAETV 179
                   +      ++    G         W+G   +P P+PP  EQ  I   I     
Sbjct: 122 RFFLNLFRTDAYMGEVDKFSHGIVKDRNRLYWEGFKQMPSPVPPPDEQAAIVRFIDHADR 181

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
           RI   I  + + I+LL+E+KQA++   VT+GL+P+V++K SG+EW+G VP+HWE++    
Sbjct: 182 RIKCYIRAKQKLIKLLEEQKQAIIHRAVTRGLDPNVRLKPSGVEWLGDVPEHWEMRRLKT 241

Query: 240 LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP-------ESYETYQIVDPGEIV 292
           L                  +  G+ I  +    +G  P         Y T      G+ V
Sbjct: 242 LC----------------RMRSGDGITAMAIEPVGDYPVYGGNGVRGY-TSNFTHDGDFV 284

Query: 293 FRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSG 352
                L   + +L     + RG   ++  AV         L W      +  +     + 
Sbjct: 285 -----LIGRQGALCGNVHLARGRFWASEHAVVASLSSGYILEWFAAILMVMNLNQYSIAA 339

Query: 353 LRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIA 412
            +  L  E V  L + VPP  +Q  I   I  ET+ I+ +V +  + I  L E R+  IA
Sbjct: 340 AQPGLAVERVLNLWLPVPPADDQKRIATQIEDETSDINQVVGRARREIEFLIEYRTRLIA 399

Query: 413 AAVTGQIDLR 422
             VTG+ D+R
Sbjct: 400 DVVTGKRDVR 409



 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/214 (22%), Positives = 88/214 (41%), Gaps = 8/214 (3%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L P    KDSG+ W+G VP  W +     L  + N      +    +SL  G  ++ L+ 
Sbjct: 5   LTPYPAYKDSGVPWLGEVPLTWSISRNGGLFIQRNETGFAHLPILEVSLKTGVRVRNLDG 64

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGID 329
                     + Y+     ++ +  + +      +        G+++ AY+  +P  G++
Sbjct: 65  SGRKQIMSDRDKYKRARKDDLAYNMMRMWQGAIGIAPTD----GLVSPAYVVARPLKGVE 120

Query: 330 STYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVET 386
             +   L R+            G+   R  L +E  K++P  VPP  EQ  I   I+   
Sbjct: 121 PRFFLNLFRTDAYMGEVDKFSHGIVKDRNRLYWEGFKQMPSPVPPPDEQAAIVRFIDHAD 180

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            RI   +   ++ I LL+E++ + I  AVT  +D
Sbjct: 181 RRIKCYIRAKQKLIKLLEEQKQAIIHRAVTRGLD 214


>gi|319775047|ref|YP_004137535.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae F3047]
 gi|317449638|emb|CBY85844.1| Putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae F3047]
          Length = 419

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 118/436 (27%), Positives = 200/436 (45%), Gaps = 37/436 (8%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           + Y  YKDSGV W+G +P HW+   +KR  +L   +  +       + L       GK +
Sbjct: 2   RRYESYKDSGVDWLGEVPSHWE---LKRLKQLFVEKKHKQS-----LSLNCGAISFGKVI 53

Query: 65  PK-DGNSRQSDTSTVSIFAKGQILYGKLGPY-----LRKAIIADFDGICSTQFLVLQPKD 118
            K D    ++   +     KG+ L   L        LR A+ ++ D + S  ++VL+ K 
Sbjct: 54  EKSDDKVTEATKRSYQEVLKGEFLINPLNLNYDLISLRIAL-SEIDVVVSAGYIVLKEKQ 112

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           ++ +    +LL       ++ +  G   +  ++  I +  + IPPL+EQ  I + +  +T
Sbjct: 113 IINKKYFSYLLHRYDVAYMKLLGSGVRQT-INYGHISDSILVIPPLSEQQKIAQFLDDKT 171

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID  +    + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HWEV    
Sbjct: 172 AKIDQAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWEVVSMK 231

Query: 239 ALVTEL-----------NRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
            +V E            N  N   ++ +  S +    I K    ++  K    + + IV 
Sbjct: 232 RVVKEHSGNGFPIDLQGNNGNIPFLKVSNFSENQDKYIFKW-NNSVTNKVIKQKKWNIVP 290

Query: 288 PGEIVFRFID--LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKV 345
              IV   I   L+ + R + S       II +  + ++    D  +  +L  + D   +
Sbjct: 291 KNSIVTAKIGEALRKNHRKILSID----SIIDNNCLGIEIKKADVLFGYYLHCALDF-DL 345

Query: 346 FYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
           F     G   SL  +  +   +++PP +EQ +I + +  +TA+ID  +      I  LKE
Sbjct: 346 F--TNPGTIPSLAMDKYRNQKIVLPPFQEQQEIADYLEQQTAKIDQAIALKTAHIEKLKE 403

Query: 406 RRSSFIAAAVTGQIDL 421
            +S  I   VTG++ +
Sbjct: 404 YKSVLINDVVTGKVQV 419


>gi|260552461|ref|ZP_05825837.1| type I restriction-modification system specificity determinant
           [Acinetobacter sp. RUH2624]
 gi|260405268|gb|EEW98764.1| type I restriction-modification system specificity determinant
           [Acinetobacter sp. RUH2624]
          Length = 461

 Score =  124 bits (311), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 106/348 (30%), Positives = 177/348 (50%), Gaps = 23/348 (6%)

Query: 93  PYLRKAIIAD-FDG-ICSTQFLVLQPKDVLPEL-LQGWLLSID-VTQRIEAICEGATMSH 148
           P  R A+++D +D  +     + L P   L +L    W ++ D V +  E +  G T   
Sbjct: 103 PVARAAVVSDEYDEYVIVADCVKLSPDLELVDLNFLIWAINSDCVRENAELVSTGTTRIR 162

Query: 149 ADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            +   +  + +P P L+EQV IR+ +  ET +IDTLI ++   I LLKEK+QA++S+ VT
Sbjct: 163 INLGELKKLKVPYPSLSEQVKIRQYLDHETAKIDTLIAKQEELIALLKEKRQAVISHAVT 222

Query: 209 KGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESN--ILSLSYGNIIQ 266
           KGLNP+V MKDSG+EW+G VP+HW V   F  ++++ R  +     +  + +  Y   + 
Sbjct: 223 KGLNPNVPMKDSGVEWLGEVPEHWTVSK-FGYISQVVRGGSPRPAGDPALFNGDYSPWVT 281

Query: 267 KLE-TRNMGLKPESYETYQIVDPGEIVFRF----IDLQNDKRSLRSAQVM------ERGI 315
             E T++  L   S ET+      E    F    + L N   +L   +++        G+
Sbjct: 282 VAEITKDDELYLTSTETFLTKKGSEQCRVFQSGTLLLSNSGATLGVPKILSINANANDGV 341

Query: 316 ITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQ 375
           +    + +    I+  Y    + + DL +     GSG + +L  + VK +P+ +PP  E 
Sbjct: 342 VGFEDLKID---IEYAYFYLSILTNDL-RERVKQGSG-QPNLNTDIVKAIPIAIPPENEI 396

Query: 376 FDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
             I   I  +      L+   E++I L++ERR++ I+A VTG+ID+R 
Sbjct: 397 KKIVVDIKKKIDHFSKLMGSAEKAIQLMQERRTALISAVVTGKIDVRN 444



 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/215 (22%), Positives = 93/215 (43%), Gaps = 26/215 (12%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTSESGKDIIYIG-----------LEDVE- 57
           KDSGV+W+G +P+HW V      ++ +  G    +G   ++ G            +D E 
Sbjct: 232 KDSGVEWLGEVPEHWTVSKFGYISQVVRGGSPRPAGDPALFNGDYSPWVTVAEITKDDEL 291

Query: 58  --SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
             + T  +L K G+ +        +F  G +L    G  L    I   +   +   +  +
Sbjct: 292 YLTSTETFLTKKGSEQ------CRVFQSGTLLLSNSGATLGVPKILSINANANDGVVGFE 345

Query: 116 PKDVLPELLQGWL--LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
              +  E    +L  L+ D+ +R++   +G+   + +   +  IP+ IPP  E   I   
Sbjct: 346 DLKIDIEYAYFYLSILTNDLRERVK---QGSGQPNLNTDIVKAIPIAIPPENEIKKIVVD 402

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           I  +      L+    + I+L++E++ AL+S +VT
Sbjct: 403 IKKKIDHFSKLMGSAEKAIQLMQERRTALISAVVT 437


>gi|145635506|ref|ZP_01791206.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae PittAA]
 gi|145267271|gb|EDK07275.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae PittAA]
          Length = 348

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 91/328 (27%), Positives = 162/328 (49%), Gaps = 15/328 (4%)

Query: 100 IADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPM 159
           +++ D + S  ++VL+ K ++ +    +LL       ++ +  G   +  ++  I +  +
Sbjct: 24  LSEIDVVVSAGYIVLKEKQIINKKYFSYLLHRYDVAYMKLLGSGVRQT-INYGHISDSIL 82

Query: 160 PIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKD 219
            IPPL+EQ  I + +  +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KD
Sbjct: 83  VIPPLSEQQKIAQFLDDKTAKIDRAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKD 142

Query: 220 SGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILS-LSYGNIIQKLETRNMGLKPE 278
           SG+EW+G VP+HW+V+    +  ++ RK  +  E  I++    G +  +   R  G    
Sbjct: 143 SGVEWIGQVPEHWDVQRSKFIFKKIERKVNE--EDQIVTCFRDGQVTLRANRRTEGFTNA 200

Query: 279 SYET-YQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG---IDSTYLA 334
             E  YQ +  G++V   +D       +  +     G  T  Y    PH    ID  + A
Sbjct: 201 LKEHGYQGIRKGDLVIHAMDAFAGAIGISDSD----GKATPVYSVCLPHNKQKIDVYFYA 256

Query: 335 WLMRSYDLCKVFYAMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
           + +R+  L     ++  G+R+     ++ D   L + +PP  EQ  I + ++ +T++ID 
Sbjct: 257 YYLRNLALSGFISSLAKGIRERSTDFRYADFAELLLPIPPYLEQQKIADYLDKQTSKIDQ 316

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           ++      I  LKE +S  I   VTG++
Sbjct: 317 VIALKTAHIEKLKEYKSVLINDVVTGKV 344



 Score = 60.5 bits (145), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 51/203 (25%), Positives = 90/203 (44%), Gaps = 7/203 (3%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           KDSGV+WIG +P+HW V   K   K    + +E  +D I     D +         +G +
Sbjct: 141 KDSGVEWIGQVPEHWDVQRSKFIFKKIERKVNE--EDQIVTCFRDGQVTLRANRRTEGFT 198

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGW 127
                       KG ++   +  +     I+D DG  +  + V  P +   +       +
Sbjct: 199 NALKEHGYQGIRKGDLVIHAMDAFAGAIGISDSDGKATPVYSVCLPHNKQKIDVYFYAYY 258

Query: 128 LLSIDVTQRIEAICEGATMSHADWK--GIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
           L ++ ++  I ++ +G      D++      + +PIPP  EQ  I + +  +T +ID +I
Sbjct: 259 LRNLALSGFISSLAKGIRERSTDFRYADFAELLLPIPPYLEQQKIADYLDKQTSKIDQVI 318

Query: 186 TERIRFIELLKEKKQALVSYIVT 208
             +   IE LKE K  L++ +VT
Sbjct: 319 ALKTAHIEKLKEYKSVLINDVVT 341


>gi|310658568|ref|YP_003936289.1| restriction modification system DNA specificity domain [Clostridium
           sticklandii DSM 519]
 gi|308825346|emb|CBH21384.1| Restriction modification system DNA specificity domain [Clostridium
           sticklandii]
          Length = 405

 Score =  124 bits (310), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 114/429 (26%), Positives = 189/429 (44%), Gaps = 53/429 (12%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESG--TGKY----- 63
           KDS + W+G   + W +VP+K    + TG+             +DV  G   G+Y     
Sbjct: 5   KDSELLWLGEYNETWDLVPLKHLVNITTGK-------------KDVNQGHPDGEYPFFTC 51

Query: 64  --LPKDGNSRQSDTSTVSIFAKGQILY-----GKLGPYLRKAIIADFDGICSTQFLVLQP 116
              P   ++   D+  + +   G + +     GK   Y R  +++DF  I       L  
Sbjct: 52  SMTPYRSSNYSFDSEALLVAGNGMVGFTQYYNGKFEAYQRTYVLSDFKEIHP-----LYL 106

Query: 117 KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
           K  + ELL  +L    V   I+ I  G      D K  G +    P + +Q  I   +  
Sbjct: 107 KHYITELLPKYLTDKSVGSVIDFIKLG------DLKSFGIVR---PSITDQKKISSYLEQ 157

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           +   ID ++ +  + IE  K+ KQ+L++  VTKGLNPDVKMKD GIEW+G +P+ W+V  
Sbjct: 158 KVALIDNILEKTKQSIEEYKKYKQSLITETVTKGLNPDVKMKDIGIEWIGEIPEQWKVLK 217

Query: 237 FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFI 296
               + E++++ +  +  ++LS++   +  K  T N G     Y  YQ V   + V   +
Sbjct: 218 -LKCIFEISKRISGELGHSVLSVTQNGLKIKDLTSNEGQLSSDYSKYQYVYKTDFVMNHM 276

Query: 297 DLQNDKRSLRSAQVMERGIITSAYMAVK-PHGIDST--YLAWLMRSYDLCKVFYAMGSGL 353
           DL      L        G+ +  Y   K   G+  +  Y  ++ +   L ++FY +G G+
Sbjct: 277 DLLTGWVDLSPYD----GVTSPDYRVFKMKDGLKYSKEYYLYIFQVCYLNQIFYGLGQGI 332

Query: 354 ----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSS 409
               R  L+ +      + VPPI EQ  I   +  +   I+  V+  E  +  L+  + S
Sbjct: 333 SNLGRWRLQTDKFINFSLPVPPIDEQKKIAKFLQNKLGEIEKFVKTKESLLKELEAYKKS 392

Query: 410 FIAAAVTGQ 418
            I   VTG+
Sbjct: 393 LIYEVVTGK 401


>gi|310639248|ref|YP_003944007.1| restriction endonuclease S subunit [Ketogulonicigenium vulgare Y25]
 gi|308752824|gb|ADO43968.1| putative restriction endonuclease S subunit [Ketogulonicigenium
           vulgare Y25]
          Length = 376

 Score =  124 bits (310), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 88/273 (32%), Positives = 148/273 (54%), Gaps = 10/273 (3%)

Query: 154 IGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNP 213
           I N+ +P+PP + Q  I   +  ET  IDTLI  +   ++L+ EK++A+V+  V +GL+P
Sbjct: 105 IANLSIPVPPSSTQHAIALFLNRETADIDTLIAAKQSLLDLMAEKRRAIVAETVMRGLDP 164

Query: 214 DVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNM 273
            V ++ SGIEW+G +P HWE++    L TE +++ ++  +  +L++S+   +     +++
Sbjct: 165 SVPLRPSGIEWLGDIPAHWEIERSRWLFTERDQR-SQTGKEEMLTVSHLTGVTPRSEKDV 223

Query: 274 GL-KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDST 331
            + + ES   Y++   G++      L     ++ +A+V   GI++ AY    P   +   
Sbjct: 224 NMFEAESTAGYKLCLAGDLAIN--TLWAWMGAMGTARV--DGIVSPAYNVYTPGPRLLPD 279

Query: 332 YLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
           Y+  L+R +   +       G+   R  L  E        VPP+ EQ  I   I+ ET +
Sbjct: 280 YVDALVRIHVFAQEVTRYSKGVWSSRLRLYPEGFFETWWPVPPLDEQQQIVEHISAETTK 339

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           ID L    E SI LLKERR++ IAAAVTGQI++
Sbjct: 340 IDRLRAATENSIALLKERRAALIAAAVTGQIEI 372



 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 97/210 (46%), Gaps = 23/210 (10%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT--SESGKDIIYIGLEDVESGTGKYLPKDG 68
           + SG++W+G IP HW+   I+R   L T R   S++GK+ + + +  + +G      KD 
Sbjct: 169 RPSGIEWLGDIPAHWE---IERSRWLFTERDQRSQTGKEEM-LTVSHL-TGVTPRSEKDV 223

Query: 69  NSRQSD-TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGW 127
           N  +++ T+   +   G +    L  ++     A  DGI S  + V  P    P LL  +
Sbjct: 224 NMFEAESTAGYKLCLAGDLAINTLWAWMGAMGTARVDGIVSPAYNVYTPG---PRLLPDY 280

Query: 128 LLSIDVTQRIEAICEGAT-MSHADW--------KGIGNIPMPIPPLAEQVLIREKIIAET 178
              +D   RI    +  T  S   W        +G      P+PPL EQ  I E I AET
Sbjct: 281 ---VDALVRIHVFAQEVTRYSKGVWSSRLRLYPEGFFETWWPVPPLDEQQQIVEHISAET 337

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVT 208
            +ID L       I LLKE++ AL++  VT
Sbjct: 338 TKIDRLRAATENSIALLKERRAALIAAAVT 367



 Score = 37.7 bits (86), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 34/70 (48%)

Query: 351 SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
           S  +  +  E +  L + VPP   Q  I   +N ETA ID L+   +  + L+ E+R + 
Sbjct: 94  SAAQPGIAVEVIANLSIPVPPSSTQHAIALFLNRETADIDTLIAAKQSLLDLMAEKRRAI 153

Query: 411 IAAAVTGQID 420
           +A  V   +D
Sbjct: 154 VAETVMRGLD 163


>gi|260428510|ref|ZP_05782489.1| type I restriction-modification system, S subunit [Citreicella sp.
           SE45]
 gi|260423002|gb|EEX16253.1| type I restriction-modification system, S subunit [Citreicella sp.
           SE45]
          Length = 426

 Score =  123 bits (308), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 120/426 (28%), Positives = 183/426 (42%), Gaps = 25/426 (5%)

Query: 20  AIPKHWKVVPIKRFTKLNTGRTSES----GKDIIYIGLEDVESGT-GKYLPKD-GNSRQS 73
           ++P H+  +PI    K N G   +      KD+   G   + +G  G    KD G    S
Sbjct: 6   SVPSHYIKLPIIAVAKKNGGIFIDGDWIESKDLSDSGFRYLTTGNVGAGEFKDQGTGYIS 65

Query: 74  DTS----TVSIFAKGQILYGKLG-PYLRKAIIADFDG--ICSTQFLVLQPKDVLPELLQG 126
           D++      +    G IL  +L  P  R  I+ D     + +   ++++P D        
Sbjct: 66  DSTFHRLRCTEVMPGDILVSRLNLPIGRACIVPDVGERMVTAVDNVIIRPSDEFDRRFLV 125

Query: 127 WLLSIDVTQRIEA-ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
           +L S      + A +  G TM       +G   + +PP  EQ  I   +  ET R+D LI
Sbjct: 126 FLFSAQHHSEMMANLARGTTMQRVSRSALGRARVYLPPFEEQTAIANYLDLETARLDGLI 185

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN 245
            ++ RFIELLKEK  A     VT   +    M+ SGI+W   +P  W V+    L  E+ 
Sbjct: 186 EKKGRFIELLKEKALAYSDRCVTGQTDSARDMRTSGIQWSPQLPAEWGVRRGKDLFREMA 245

Query: 246 RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET-YQIVDPGEIVFRFIDLQNDKRS 304
           R   +  +  I +   G +  +   R  G      E  YQ +  G++V   +D       
Sbjct: 246 RP-VRSDDEIITAFRDGQVCLRSRRRTEGYTFAEKEVGYQRILKGDLVIHTMDAFAGAIG 304

Query: 305 LRSAQVMERGIITSAYMAVKPHGID--STYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFED 361
           +      + G  T  Y    P   D    Y A ++R        + +   +R+ + +F  
Sbjct: 305 ISE----DNGKATGEYAVCTPKSPDIIPEYYALILRCMARRNYIFVLCPSVRERAPRFRF 360

Query: 362 VKRLPVL--VPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           V+  PV+  VPP  EQ  I   I   T R   L+ K E+SI LLKE+RS+ I AAVTG+I
Sbjct: 361 VRFAPVMLPVPPRAEQEQIVASIEEHTRRAKALIAKTERSIELLKEKRSALITAAVTGKI 420

Query: 420 DLRGES 425
           D+R  +
Sbjct: 421 DVRSAA 426



 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 83/202 (41%), Gaps = 6/202 (2%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           + SG+QW   +P  W V   K   +    R   S  +II     D +         +G +
Sbjct: 218 RTSGIQWSPQLPAEWGVRRGKDLFR-EMARPVRSDDEII-TAFRDGQVCLRSRRRTEGYT 275

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK--DVLPELLQGWL 128
                       KG ++   +  +     I++ +G  + ++ V  PK  D++PE     L
Sbjct: 276 FAEKEVGYQRILKGDLVIHTMDAFAGAIGISEDNGKATGEYAVCTPKSPDIIPEYYALIL 335

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIP--MPIPPLAEQVLIREKIIAETVRIDTLIT 186
             +     I  +C         ++ +   P  +P+PP AEQ  I   I   T R   LI 
Sbjct: 336 RCMARRNYIFVLCPSVRERAPRFRFVRFAPVMLPVPPRAEQEQIVASIEEHTRRAKALIA 395

Query: 187 ERIRFIELLKEKKQALVSYIVT 208
           +  R IELLKEK+ AL++  VT
Sbjct: 396 KTERSIELLKEKRSALITAAVT 417


>gi|291566232|dbj|BAI88504.1| type I restriction-modification system S subunit [Arthrospira
           platensis NIES-39]
          Length = 396

 Score =  122 bits (307), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 87/280 (31%), Positives = 138/280 (49%), Gaps = 26/280 (9%)

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           IPPL EQ  I   +  ET +ID LI  + R ++LL EK++AL+++ VT+GLNPDV M+DS
Sbjct: 124 IPPLGEQKAIAHYLDKETAKIDQLIEAKKRLLQLLDEKRRALITHTVTRGLNPDVPMRDS 183

Query: 221 GIEWVGLVPDHWEVKPF-----FALVTELNRKNTKLIESNILSLSYGN-----IIQKLET 270
           G+EW+G +P HW+           L   L  +   L +  +  L   +     I+   E 
Sbjct: 184 GVEWIGKIPKHWKCSKIKHHYEITLGKMLQNEPHSLEDVEVPYLKSQHVQSDRILMDNEL 243

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI-D 329
             M   P       ++    +V    ++   + ++ S++  +  II +A   V+P    D
Sbjct: 244 PQMWANPWEIANLNVIKGDLLVCEGGEI--GRSAIISSKPPDNCIIQNALHLVRPKPTGD 301

Query: 330 STYLAWLM------RSYD-LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVI 382
             +L +L+      R  D LC                E   ++ + +PP+ EQ  I N +
Sbjct: 302 VNFLKYLLNHAISQRWLDVLC------NKATIAHFTVEKFSQMSIELPPLSEQKAIANYL 355

Query: 383 NVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           + ETA+I+ L   +  +I LL+ERR+S I AAVTGQI  +
Sbjct: 356 DKETAKINQLRSAVRDTITLLQERRTSLITAAVTGQIQTK 395



 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 101/213 (47%), Gaps = 19/213 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           +DSGV+WIG IPKHWK   IK   ++  G+  ++        LEDVE    K      + 
Sbjct: 181 RDSGVEWIGKIPKHWKCSKIKHHYEITLGKMLQNEPH----SLEDVEVPYLKSQHVQSDR 236

Query: 71  RQSDTSTVSIFA-----------KGQILYGKLGPYLRKAIIADF---DGICSTQFLVLQP 116
              D     ++A           KG +L  + G   R AII+     + I      +++P
Sbjct: 237 ILMDNELPQMWANPWEIANLNVIKGDLLVCEGGEIGRSAIISSKPPDNCIIQNALHLVRP 296

Query: 117 KDVLPELLQGWLLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           K         +LL+  ++QR ++ +C  AT++H   +    + + +PPL+EQ  I   + 
Sbjct: 297 KPTGDVNFLKYLLNHAISQRWLDVLCNKATIAHFTVEKFSQMSIELPPLSEQKAIANYLD 356

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            ET +I+ L +     I LL+E++ +L++  VT
Sbjct: 357 KETAKINQLRSAVRDTITLLQERRTSLITAAVT 389



 Score = 43.5 bits (101), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 44/93 (47%), Gaps = 4/93 (4%)

Query: 328 IDST----YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
           ID+T    +L WL        +           L  +D     V +PP+ EQ  I + ++
Sbjct: 79  IDATTTHHHLRWLFYLLQTLNLDQGTDEAAVPGLSRDDAYAKKVFIPPLGEQKAIAHYLD 138

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
            ETA+ID L+E  ++ + LL E+R + I   VT
Sbjct: 139 KETAKIDQLIEAKKRLLQLLDEKRRALITHTVT 171


>gi|229520170|ref|ZP_04409597.1| restriction modification system DNA specificity domain [Vibrio
           cholerae TM 11079-80]
 gi|229342764|gb|EEO07755.1| restriction modification system DNA specificity domain [Vibrio
           cholerae TM 11079-80]
          Length = 434

 Score =  122 bits (306), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 123/432 (28%), Positives = 203/432 (46%), Gaps = 50/432 (11%)

Query: 25  WKVVPIKR-FT---KLNTG-----RTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75
           W +VP KR FT   ++N G     R + + K +I   L+D++             + SD 
Sbjct: 16  WNLVPAKRLFTSSKEINQGMKESNRLALTMKGVINRSLDDLQG-----------LQSSDY 64

Query: 76  STVSIFAKGQILYGKLG----PYLRKAIIADFDGICSTQFLVLQP--KDVLPELLQGWLL 129
           S   IF K  +++  +        R  I+ +  GI S  ++ +      + P     +  
Sbjct: 65  SVYQIFEKDDLVFKLIDLENIKTSRVGIVHE-RGIMSPAYIRVSACSNSIYPRFYYWYFF 123

Query: 130 SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERI 189
           ++ +T  I     G    +     +  IP+P+  ++ Q  +   +  ET RID+LI E+ 
Sbjct: 124 ALYLTN-IYNKLGGGVRQNLTAGDLLEIPVPLIDISLQKQVSAFLDRETQRIDSLIEEKQ 182

Query: 190 RFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT 249
            FI LLKEK+QAL+S++VTKGLNP+V+M+DSGIEW+G VP HW VK     V  + +  +
Sbjct: 183 TFITLLKEKRQALISHVVTKGLNPNVEMQDSGIEWIGQVPKHWVVKKIKYDVLGIEQGWS 242

Query: 250 KLIESNILSLSYGNIIQKLETRNMGL--------KPESYETYQ--IVDPGEIVFRFIDLQ 299
              ES  +   +   + K+   N G+         PE  E  +   +  G++    +   
Sbjct: 243 PQCESTPVPDDHTWGVVKVGCVNRGIFNPEQNKKLPEELEPRKEYAIKKGDL---LVSRA 299

Query: 300 NDKRSLRSAQVMERG-----IITSAY-MAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGL 353
           N K  + SA V +R      +    Y + +     D  + A+ + S    +      +G 
Sbjct: 300 NAKEWVGSAAVPDRDYDNLLLCDKIYRIKLDLEKADPEFFAYYLASDQAREQIEIDATGT 359

Query: 354 RQSL---KFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
             S+       +  +P+  P + EQ  I   I  +T++ID L+ ++  SI LLKE R+S 
Sbjct: 360 SSSMLNIGQGTILNMPIPAPELPEQQSIVRGIKNKTSQIDRLMLEVLDSIELLKEHRTSL 419

Query: 411 IAAAVTGQIDLR 422
           I+AAVTG+ID+R
Sbjct: 420 ISAAVTGKIDVR 431



 Score =  100 bits (248), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 65/197 (32%), Positives = 103/197 (52%), Gaps = 3/197 (1%)

Query: 232 WEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEI 291
           W + P   L T     N  + ESN L+L+   +I +      GL+   Y  YQI +  ++
Sbjct: 16  WNLVPAKRLFTSSKEINQGMKESNRLALTMKGVINRSLDDLQGLQSSDYSVYQIFEKDDL 75

Query: 292 VFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP--HGIDSTYLAWLMRSYDLCKVFYAM 349
           VF+ IDL+N K S R   V ERGI++ AY+ V    + I   +  W   +  L  ++  +
Sbjct: 76  VFKLIDLENIKTS-RVGIVHERGIMSPAYIRVSACSNSIYPRFYYWYFFALYLTNIYNKL 134

Query: 350 GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSS 409
           G G+RQ+L   D+  +PV +  I  Q  ++  ++ ET RID L+E+ +  I LLKE+R +
Sbjct: 135 GGGVRQNLTAGDLLEIPVPLIDISLQKQVSAFLDRETQRIDSLIEEKQTFITLLKEKRQA 194

Query: 410 FIAAAVTGQIDLRGESQ 426
            I+  VT  ++   E Q
Sbjct: 195 LISHVVTKGLNPNVEMQ 211



 Score = 59.7 bits (143), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 99/222 (44%), Gaps = 27/222 (12%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIK-RFTKLNTGRTSESGKD---------IIYIGLED--- 55
           + +DSG++WIG +PKHW V  IK     +  G + +             ++ +G  +   
Sbjct: 209 EMQDSGIEWIGQVPKHWVVKKIKYDVLGIEQGWSPQCESTPVPDDHTWGVVKVGCVNRGI 268

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGP--YLRKAIIADFDG----ICST 109
                 K LP++   R+          KG +L  +     ++  A + D D     +C  
Sbjct: 269 FNPEQNKKLPEELEPRKE-----YAIKKGDLLVSRANAKEWVGSAAVPDRDYDNLLLCDK 323

Query: 110 QFLV-LQPKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAE 166
            + + L  +   PE    +L S    ++IE    G  ++M +     I N+P+P P L E
Sbjct: 324 IYRIKLDLEKADPEFFAYYLASDQAREQIEIDATGTSSSMLNIGQGTILNMPIPAPELPE 383

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           Q  I   I  +T +ID L+ E +  IELLKE + +L+S  VT
Sbjct: 384 QQSIVRGIKNKTSQIDRLMLEVLDSIELLKEHRTSLISAAVT 425


>gi|228930124|ref|ZP_04093134.1| hypothetical protein bthur0010_48060 [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228829623|gb|EEM75250.1| hypothetical protein bthur0010_48060 [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
          Length = 418

 Score =  121 bits (304), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 109/435 (25%), Positives = 201/435 (46%), Gaps = 48/435 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           KDS ++WIGAIP +WKVVP   F   N+ +  E   + +    +       +++  +   
Sbjct: 2   KDSKIEWIGAIPNYWKVVPSNLFF-YNSSKKVEGNVEQLTASQKYGVISQSRFMKLESQM 60

Query: 71  --RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK----------- 117
             ++ D S +    KG  +   L  +     IA   G  +  + VL+ K           
Sbjct: 61  PVQKRDLSDLKQVDKGDFVIS-LRSFQGGLEIAQESGGITPAYTVLKEKTKQTYAGYYKY 119

Query: 118 ----DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
               ++  + L+G +L        + I +G  +  +++     +P+ +PPL EQ  I E 
Sbjct: 120 FFKSEMYIQALRGTVL--------DTIRDGKAIRFSNF---SMVPIVLPPLNEQKKIVEV 168

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW- 232
           +  +T  I+ +I++  + I+ LK+ KQ+L++  VTKGLN +V +KDS IEW+G +P  W 
Sbjct: 169 LDEKTKTINNIISDTQQSIKELKKYKQSLITEAVTKGLNRNVGIKDSEIEWIGEMPKEWN 228

Query: 233 --EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
             +V   FA+   +  +N      ++LS++   +  K  TRN G     Y  YQIV P +
Sbjct: 229 LVKVNRLFAIKKNIANQNG----YDVLSVTQSGLKVKDITRNEGQMAADYSKYQIVKPKD 284

Query: 291 IVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLC---KVFY 347
            V   +DL      + +    + G+ +  Y        +     + +  + +C   ++FY
Sbjct: 285 FVMNHMDLLTGWIDIAA----QEGVTSPDYRVFYTKDTELVSNEFYLYVFQICYTNRIFY 340

Query: 348 AMGSGL----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
            +G G+    R  L+ +      + +PP+ EQ  I   +N +   I+ ++E+ +  +  L
Sbjct: 341 GLGQGVSNLGRWRLQTDKFLNFYLPLPPVNEQQAIVKFLNGKLVEINSMIEQKKDLLGEL 400

Query: 404 KERRSSFIAAAVTGQ 418
           ++ + S I   VTG+
Sbjct: 401 EQYKKSLIYECVTGK 415



 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 105/210 (50%), Gaps = 17/210 (8%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQ----KLETRN 272
           MKDS IEW+G +P++W+V P        ++K    +E    S  YG I Q    KLE++ 
Sbjct: 1   MKDSKIEWIGAIPNYWKVVPSNLFFYNSSKKVEGNVEQLTASQKYGVISQSRFMKLESQ- 59

Query: 273 MGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTY 332
           M ++       + VD G+ V   I L++ +  L  AQ  E G IT AY  +K      TY
Sbjct: 60  MPVQKRDLSDLKQVDKGDFV---ISLRSFQGGLEIAQ--ESGGITPAYTVLKEK-TKQTY 113

Query: 333 LAWLMRSYDLCKVFYAM-GSGLR-----QSLKFEDVKRLPVLVPPIKEQFDITNVINVET 386
             +    +       A+ G+ L      ++++F +   +P+++PP+ EQ  I  V++ +T
Sbjct: 114 AGYYKYFFKSEMYIQALRGTVLDTIRDGKAIRFSNFSMVPIVLPPLNEQKKIVEVLDEKT 173

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
             I+ ++   +QSI  LK+ + S I  AVT
Sbjct: 174 KTINNIISDTQQSIKELKKYKQSLITEAVT 203


>gi|218680840|ref|ZP_03528737.1| type I restriction-modification system specificity determinant
           [Rhizobium etli CIAT 894]
          Length = 482

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 144/272 (52%), Gaps = 8/272 (2%)

Query: 155 GNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPD 214
           G++ +P+P L  Q  I   +  ET RID LI  + R +E+L+E+K A+    +  GL+  
Sbjct: 1   GSVNIPVPDLDAQRAIAAFLDRETTRIDKLIETKERQVEVLREQKSAITKEYIHSGLHAG 60

Query: 215 VKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMG 274
            +   +   W  L+P  W+ +    L     R+    ++   +   +G I++     N+ 
Sbjct: 61  RERVATQNSWFPLIPQGWQPRRMRFLFRAAKRQGMPDLDVLSVYRDFGVILKSSRDDNIN 120

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYL 333
             PE   +YQ+V+PG++V     ++  + SL  +++  RGI +  Y+  +P   ++  Y+
Sbjct: 121 KTPEDLSSYQLVEPGDLVVN--KMKAWQGSLGISEL--RGITSPDYLVYRPVAPMNGRYM 176

Query: 334 AWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVL--VPPIKEQFDITNVINVETARID 390
            +L+R+  +  +F  + +G+R    + E  K + V+  +P + EQ +I   I+  T+RI+
Sbjct: 177 HYLLRTRPMPSLFLTISNGIRIDQWRLEHAKFMDVVAWLPSLDEQAEIAAAIDARTSRIE 236

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            +V+ +  SI LL+E R++ I AAV G ID+R
Sbjct: 237 RIVKSVSDSIELLREHRAALITAAVAGHIDIR 268


>gi|309776566|ref|ZP_07671546.1| type I restriction-modification system specificity determinant
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308915667|gb|EFP61427.1| type I restriction-modification system specificity determinant
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 457

 Score =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 110/437 (25%), Positives = 192/437 (43%), Gaps = 29/437 (6%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGKD------IIYIGLEDVE 57
           K Y  YK   ++W   IP  W VVP+KR F+ + +G T +S  +      + +I   D+ 
Sbjct: 2   KTYSDYKKCKIKWCPTIPSSWDVVPLKRIFSNIGSGATPKSNNNNYYGGNVSWIQSGDLH 61

Query: 58  ----SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV 113
               S T K +    +S   D S + I+    I     G  +    I+  D  C+ Q   
Sbjct: 62  NHFLSSTKKRI---TDSALRDVSALKIYKTPFISIAMYGASIGNLSISKIDS-CTNQACC 117

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
                        +LLS      + ++  G T  +     I N+ +P+P + EQ  I   
Sbjct: 118 NMSGSAGNIEYFYYLLS-SCKDYMISLSAGGTQPNISQLIIKNLILPLPSVNEQDQIVRF 176

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  +   I+ LI  + + I  ++E K+ +++  VT GLN +V MK SG+EW+G +P+HW+
Sbjct: 177 LDWKVSEINKLINVKEKEIVQIQELKKTVINDAVTHGLNRNVPMKYSGVEWLGDIPEHWK 236

Query: 234 VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETR--NMGLKPESYETYQIVDPGEI 291
           +     ++   + KN   +    +    G I++ ++ +  N    P+    Y++V  G+ 
Sbjct: 237 IIKLRKILHPFSEKNHPELPLLSVVREKGVIVRDVDDKESNHNFIPDDLSGYKMVKKGQF 296

Query: 292 VFRFIDLQNDKRSLRSAQVME--RGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAM 349
                   N  ++ + +  +    GI++ AY        +  Y  + +RS      F   
Sbjct: 297 AM------NKMKAWQGSYGVSDYTGIVSPAYFIFDVDFENLEYFHYAIRSKVYVNFFAQA 350

Query: 350 GSGLR---QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
             G+R     L    +K +P +VPP +EQ +I N I     R    +  +E  I  L E 
Sbjct: 351 SDGIRVGQWDLSMNKMKEIPFIVPPEEEQKEIVNYIPKALERYTNAINTLESQIEALHEL 410

Query: 407 RSSFIAAAVTGQIDLRG 423
           ++  I+ AVTG+ID+R 
Sbjct: 411 KNKLISDAVTGKIDVRN 427


>gi|126666657|ref|ZP_01737635.1| type I restriction-modification system, S subunit [Marinobacter sp.
           ELB17]
 gi|126629045|gb|EAZ99664.1| type I restriction-modification system, S subunit [Marinobacter sp.
           ELB17]
          Length = 429

 Score =  120 bits (301), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 103/371 (27%), Positives = 177/371 (47%), Gaps = 49/371 (13%)

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLV------LQP---KDVLPELLQGWLLSIDV 133
           +G IL  + G   R A+   FD  C  +F        ++P     +LPE +  W   + V
Sbjct: 75  RGDILVSEGGDAGRTAV---FD--CDEEFYFQNAINRIRPAGNSTILPEFIYYWFTFLKV 129

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIE 193
              +E +C  AT++H   + +   P+ +PPL  Q  I + +  +T RID LI ++   ++
Sbjct: 130 AGYVEMVCNVATIAHFTAEKVKAAPLALPPLKTQHSIAQFLDEKTARIDGLIEKKCALLD 189

Query: 194 LLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK-----------------P 236
            L EK+QAL++  +TKGL+P+  MK SG EW+G +P +WEVK                  
Sbjct: 190 RLAEKRQALITRAITKGLDPNAIMKPSGTEWLGHIPANWEVKKLRRVRRYMTSGSRDWAA 249

Query: 237 FFALVTELNRKNTKLIESNI-LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
           ++A   +   + T +    I L LS        ETR + L   +  T   V  G+I+   
Sbjct: 250 YYADEGDRFLRMTNVTGEGIELDLS--------ETRYVNLDGATEGTRTSVREGDIL--- 298

Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAV---KPHGIDSTYLAWLMRSYDLCKVFYAMG-- 350
           I +  +  ++   +    G   + ++A+    P   +S +L   + S D+ +  + +   
Sbjct: 299 ITITAELGAVAVIRKEIEGAYINQHLALFRPSPELCESGFLVNFL-STDMARAQFMLSGQ 357

Query: 351 SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
            G +Q L FE V  + +  PP++EQ  I N  +    + + + + ++ SI  L E RS+ 
Sbjct: 358 GGTKQGLGFEQVNNVIIGFPPLREQELIGNFCSEIRRQSESVEQPLKLSIDKLIEYRSAV 417

Query: 411 IAAAVTGQIDL 421
           I AAVTGQ+++
Sbjct: 418 ITAAVTGQLEI 428



 Score = 39.7 bits (91), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 99/222 (44%), Gaps = 30/222 (13%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-------SESGKDIIYI------GLEDVE 57
           K SG +W+G IP +W+V  ++R  +  T  +       ++ G   + +      G+E ++
Sbjct: 214 KPSGTEWLGHIPANWEVKKLRRVRRYMTSGSRDWAAYYADEGDRFLRMTNVTGEGIE-LD 272

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII-ADFDGICSTQFLVL-Q 115
               +Y+  DG +  + TS      +G IL          A+I  + +G    Q L L +
Sbjct: 273 LSETRYVNLDGATEGTRTSV----REGDILITITAELGAVAVIRKEIEGAYINQHLALFR 328

Query: 116 PKDVLPELLQ-GWLLSIDVTQRIEA----ICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           P    PEL + G+L++   T    A      +G T     ++ + N+ +  PPL EQ LI
Sbjct: 329 PS---PELCESGFLVNFLSTDMARAQFMLSGQGGTKQGLGFEQVNNVIIGFPPLREQELI 385

Query: 171 REKIIAETVRIDTLITERIRF-IELLKEKKQALVSYIVTKGL 211
                +E  R    + + ++  I+ L E + A+++  VT  L
Sbjct: 386 -GNFCSEIRRQSESVEQPLKLSIDKLIEYRSAVITAAVTGQL 426


>gi|322379476|ref|ZP_08053842.1| Restriction modification system DNA specificity domain
           [Helicobacter suis HS1]
 gi|322380457|ref|ZP_08054656.1| type I restriction-modification system specificity subunit
           [Helicobacter suis HS5]
 gi|321147102|gb|EFX41803.1| type I restriction-modification system specificity subunit
           [Helicobacter suis HS5]
 gi|321148083|gb|EFX42617.1| Restriction modification system DNA specificity domain
           [Helicobacter suis HS1]
          Length = 402

 Score =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 90/300 (30%), Positives = 153/300 (51%), Gaps = 18/300 (6%)

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
           ++E +  G  +   + + +  I +P+PPL EQ  I   +  +  +I   I ++ R + LL
Sbjct: 105 QLEHLKTGGGVPGLNREHVYQILIPLPPLKEQHAIATFLDHKCAKIVACIAKKTRMLALL 164

Query: 196 KEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF---FALVTELNRKNTKLI 252
           KE KQAL+S I TKGLNP    K SG+ W+G +P HW + P    F +  E+N+     +
Sbjct: 165 KEYKQALISKITTKGLNPQEHFKPSGVAWLGDIPGHWGLIPLGRIFKIRDEINKDRAITL 224

Query: 253 ESNILSLSYG-NIIQKLETRNMGLKPES-YETYQIVDPGEIVFRFIDLQNDKRSLRSAQV 310
              ILSL     ++   E  N+G K ++    YQ+V  G++V   ++       + +   
Sbjct: 225 ---ILSLVKDIGVLPYSEKGNIGNKAKADLSQYQVVRSGDLVLNKMNAVIGSLGVSNYD- 280

Query: 311 MERGIITSAYMAVKPHGID---STYLAWLMRSYDLCKVF--YAMG-SGLRQSLKFEDVKR 364
              G+++  Y+ +     +     Y A L  S  L +    YA G   +R+S+ F   K+
Sbjct: 281 ---GLVSPIYLVLFIQNKNLHLMQYYASLFASKALQQSLGQYAYGIMKIRESIDFMSFKQ 337

Query: 365 LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           + + VPP+KEQ  I   ++   A++D L+ K++  I  LK+ +S+ I+ AV GQI L+ +
Sbjct: 338 MLLPVPPLKEQHAIAAFLDHRLAKLDTLITKLQTQIQDLKDYKSALISEAVLGQIPLKAK 397



 Score = 73.6 bits (179), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 96/203 (47%), Gaps = 9/203 (4%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKD- 67
            +K SGV W+G IP HW ++P+ R  K+      +    +I   ++D+  G   Y  K  
Sbjct: 185 HFKPSGVAWLGDIPGHWGLIPLGRIFKIRDEINKDRAITLILSLVKDI--GVLPYSEKGN 242

Query: 68  -GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
            GN  ++D S   +   G ++  K+   +    ++++DG+ S  +LVL  ++    L+Q 
Sbjct: 243 IGNKAKADLSQYQVVRSGDLVLNKMNAVIGSLGVSNYDGLVSPIYLVLFIQNKNLHLMQY 302

Query: 127 W---LLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           +     S  + Q +     G        D+     + +P+PPL EQ  I   +     ++
Sbjct: 303 YASLFASKALQQSLGQYAYGIMKIRESIDFMSFKQMLLPVPPLKEQHAIAAFLDHRLAKL 362

Query: 182 DTLITERIRFIELLKEKKQALVS 204
           DTLIT+    I+ LK+ K AL+S
Sbjct: 363 DTLITKLQTQIQDLKDYKSALIS 385


>gi|254228173|ref|ZP_04921602.1| Restriction endonuclease S subunits [Vibrio sp. Ex25]
 gi|262394006|ref|YP_003285860.1| type I restriction-modification system specificity subunit S
           [Vibrio sp. Ex25]
 gi|151939246|gb|EDN58075.1| Restriction endonuclease S subunits [Vibrio sp. Ex25]
 gi|262337600|gb|ACY51395.1| type I restriction-modification system specificity subunit S
           [Vibrio sp. Ex25]
          Length = 437

 Score =  119 bits (299), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 109/426 (25%), Positives = 191/426 (44%), Gaps = 17/426 (3%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           + +Y D+G+ W+G+IP HW+  P+   +KL +  T+  G+ ++ + L+       +   K
Sbjct: 10  HNEYTDTGISWLGSIPSHWEAAPLCSVSKLKS-ITNHVGEPLLSVYLDKGVIRFDEVEAK 68

Query: 67  DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
             N    D S   +   G  +      +     I+   GI S  +LVLQ    +      
Sbjct: 69  RTNVTSLDLSKYQLVEPGDFVLNNQQAWRGSVGISAHRGIVSPAYLVLQLSSKIYPRFGN 128

Query: 127 WLL---SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDT 183
           +L    S+     + +   G    +  W  +    +  P L EQ+ I   +  +T +ID 
Sbjct: 129 YLFRDGSMVANYLVNSKGVGTIQRNLYWPQLKRALVFFPGLDEQIAIANYLDEKTSQIDE 188

Query: 184 LITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTE 243
            I  + + IELLKE+KQ ++   VT+GLNPDV MKDSG++W+G +P+HW V         
Sbjct: 189 AIAIKQKQIELLKERKQIIIQQAVTQGLNPDVPMKDSGVDWIGKIPEHWTVSKIGHYARV 248

Query: 244 LN----RKNTKLI--ESNILSLSYGNIIQKLETRNMGLKPESY--ETYQIVDPGEIVFRF 295
            N     ++ K    E  I  +S G +   + +    L   +   E    + P   V   
Sbjct: 249 YNGSTPSRDVKRYWDEGTIPWMSSGKVNDYIISTPSELITTAALRECSLRIFPKGTVLIG 308

Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYL-AWLMRSYDLCKVFYAMGSGLR 354
           I  Q   R   +   ++  I  +    +    I S +L  +L+++YD  +     G G  
Sbjct: 309 IVGQGKTRGTSAMLAIDAVINQNVAGIIPSEKILSEFLHQYLIQAYDEVR---NQGQGSN 365

Query: 355 Q-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAA 413
           Q +L  + +    +  P I EQ +I + I +++ ++D  ++     I  LKE +++ I +
Sbjct: 366 QEALNCQILSSFKIAFPSIIEQKEIVHFIAIQSQKLDQSIDIQFNQIEKLKEYKTTLINS 425

Query: 414 AVTGQI 419
           AVTG+I
Sbjct: 426 AVTGKI 431


>gi|71276008|ref|ZP_00652290.1| putative type I restriction enzyme, S subunit [Xylella fastidiosa
           Dixon]
 gi|71899046|ref|ZP_00681211.1| putative type I restriction enzyme, S subunit [Xylella fastidiosa
           Ann-1]
 gi|71163241|gb|EAO12961.1| putative type I restriction enzyme, S subunit [Xylella fastidiosa
           Dixon]
 gi|71731159|gb|EAO33225.1| putative type I restriction enzyme, S subunit [Xylella fastidiosa
           Ann-1]
          Length = 457

 Score =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 71/200 (35%), Positives = 108/200 (54%), Gaps = 4/200 (2%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           K SG++W+G +P HW+V  +K      T +T+   +D IY+ +E V+S TG   P +G  
Sbjct: 219 KPSGIEWLGDVPVHWEVRRLKFLASNTTSQTTTKARDEIYLAMEHVQSWTGVARPLEGEV 278

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWL 128
             +  STV  F    +L+GKL PYL K   A  +G+C ++FLVL+ +   +LP  L+  L
Sbjct: 279 EFA--STVKRFVVDDVLFGKLRPYLAKVTRAKCNGVCVSEFLVLRSRKEFILPAYLEQML 336

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITER 188
               V   I +   GA M  ADW  IGN+ +P+P    Q  I   I +ET  +   IT  
Sbjct: 337 RCKRVIDLINSSTAGAKMPRADWIFIGNVRLPVPCKDVQEAILSHIESETKDLGEAITRT 396

Query: 189 IRFIELLKEKKQALVSYIVT 208
              I+L++E +  L++ +VT
Sbjct: 397 EDEIKLIREYRDRLITDVVT 416



 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 113/439 (25%), Positives = 185/439 (42%), Gaps = 44/439 (10%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           YP Y +SG+ WI  +P+ W+V+   R   L   R      D+  +   +V   TG  +  
Sbjct: 7   YPTYCNSGLAWIPKLPEGWQVL---RNGCLFGHRVEMGFPDLPIL---EVSLRTGVRVRD 60

Query: 67  DGNSRQ----SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
             N ++    S         KG I Y  +  +     +A  DG+ S  ++V++P      
Sbjct: 61  MENLKRKQVISQKEKYKRATKGDIAYNMMRMWQGAVGLAPVDGLVSPAYVVVKPYAEANS 120

Query: 123 LLQGWLL-SIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
               +L  +    Q +     G  A  +   W+    +P  +PPL EQ  I   + A+  
Sbjct: 121 TYYSYLFRTAAYMQEVNKYSRGIVADRNRLYWESFKQMPSLVPPLPEQKQIVTYLRAQDA 180

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
            I   I  +   I+LL E+K  ++ + VT+GL+  V +K SGIEW+G VP HWEV+    
Sbjct: 181 HIARFIKAKRDLIKLLTEQKLRIIDHAVTRGLDASVALKPSGIEWLGDVPVHWEVRRLKF 240

Query: 240 LVTELNRKNTKLIESNI-LSL----SYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFR 294
           L +    + T      I L++    S+  + + LE                V+    V R
Sbjct: 241 LASNTTSQTTTKARDEIYLAMEHVQSWTGVARPLEGE--------------VEFASTVKR 286

Query: 295 FI--DLQNDKRSLRSAQVME---RGIITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVFY 347
           F+  D+   K     A+V      G+  S ++ ++     I   YL  ++R   +  +  
Sbjct: 287 FVVDDVLFGKLRPYLAKVTRAKCNGVCVSEFLVLRSRKEFILPAYLEQMLRCKRVIDLIN 346

Query: 348 AMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           +  +G    R    F    RLPV    ++E   I + I  ET  +   + + E  I L++
Sbjct: 347 SSTAGAKMPRADWIFIGNVRLPVPCKDVQEA--ILSHIESETKDLGEAITRTEDEIKLIR 404

Query: 405 ERRSSFIAAAVTGQIDLRG 423
           E R   I   VTGQ+D+RG
Sbjct: 405 EYRDRLITDVVTGQVDVRG 423


>gi|257091992|ref|YP_003165633.1| restriction modification system DNA specificity protein-containing
           protein [Candidatus Accumulibacter phosphatis clade IIA
           str. UW-1]
 gi|257044516|gb|ACV33704.1| restriction modification system DNA specificity domain protein
           [Candidatus Accumulibacter phosphatis clade IIA str.
           UW-1]
          Length = 417

 Score =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 97/330 (29%), Positives = 161/330 (48%), Gaps = 24/330 (7%)

Query: 106 ICSTQFLVLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
           I ST F V++P + L      + L +      +E+   G +    +   +G+I + +P L
Sbjct: 93  IVSTGFAVVRPSNELDHRFCKYALRASSFLWGVESRSTGVSYPAINASDLGDINVSLPEL 152

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
             Q LI   +  ET RID LI E+ R + LL+EK+ AL+S +VT+GL+P+  +K SG EW
Sbjct: 153 GAQRLIASYLDRETARIDGLIAEKERMLALLEEKRAALISRVVTRGLDPNSPLKPSGQEW 212

Query: 225 VGLVPDHWEVKPF----FALVTELNRKNTKLIE-----SNILSLSYGNIIQKLETRNMGL 275
           +G +P HW    F    F    +++ ++ + +E      N +    G +     + + G 
Sbjct: 213 LGEIPAHWPTTKFSWDVFISEGQVDPEDDRFLEMILVAPNHIESRTGEVTHTETSADQGA 272

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM-AVKPHG-IDSTYL 333
               Y   Q    G++++  I     + +LR   + E   + SA M A++P   +   YL
Sbjct: 273 MSGKYFCKQ----GDVLYSKI-----RPALRKVVLAEDDCLCSADMYALRPSKRLMPEYL 323

Query: 334 AWLMRSYDLCKVFYAMGSG--LRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
            + + S D   V+  + S       +  E    + + VPP++EQ  I   I     RID+
Sbjct: 324 QYFLLSEDF-SVWAELESARVAMPKINRETFSAIRIPVPPLEEQERIVLEIRDGAKRIDL 382

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
             + +  S+ LLKERR++ I AAV+GQI L
Sbjct: 383 QRKAVRGSVELLKERRAALITAAVSGQIPL 412



 Score = 93.6 bits (231), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 102/203 (50%), Gaps = 6/203 (2%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK---DIIYIGLEDVESGTGKYLPKD 67
           K SG +W+G IP HW          ++ G+         ++I +    +ES TG+    +
Sbjct: 206 KPSGQEWLGEIPAHWPTTKFSWDVFISEGQVDPEDDRFLEMILVAPNHIESRTGEVTHTE 265

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQG 126
            ++ Q   S      +G +LY K+ P LRK ++A+ D +CS     L+P K ++PE LQ 
Sbjct: 266 TSADQGAMSGKYFCKQGDVLYSKIRPALRKVVLAEDDCLCSADMYALRPSKRLMPEYLQY 325

Query: 127 WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
           +LLS D +   E       M   + +    I +P+PPL EQ  I  +I     RID L  
Sbjct: 326 FLLSEDFSVWAELESARVAMPKINRETFSAIRIPVPPLEEQERIVLEIRDGAKRID-LQR 384

Query: 187 ERIR-FIELLKEKKQALVSYIVT 208
           + +R  +ELLKE++ AL++  V+
Sbjct: 385 KAVRGSVELLKERRAALITAAVS 407


>gi|294637839|ref|ZP_06716110.1| restriction endonuclease S subunit [Edwardsiella tarda ATCC 23685]
 gi|291089013|gb|EFE21574.1| restriction endonuclease S subunit [Edwardsiella tarda ATCC 23685]
          Length = 284

 Score =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 80/258 (31%), Positives = 136/258 (52%), Gaps = 19/258 (7%)

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           ET +ID LI ++ + IELLKEK+QA++S+ VTKGLNPDV MKDSG+EW+G VP+HW +K 
Sbjct: 16  ETAKIDNLIEKQQQLIELLKEKRQAVISHAVTKGLNPDVPMKDSGVEWLGEVPEHWSIKS 75

Query: 237 F-FALVT------ELNRKNTKLIESNILSLSYGNIIQK---LETRNMGLKPESYETYQIV 286
           + +A +          R +  L + +   +  G++ +    +ET +  L  +     Q+ 
Sbjct: 76  YRYACLIYRGKFGHRPRNDPSLYDGDYPFIQTGDVARASKFIETYSQTLNEKGKAVSQLF 135

Query: 287 DPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY--DLCK 344
             G ++        D     +A +        + +  KP+   + +L +L  S+   L  
Sbjct: 136 PSGTLMMAIAANIGD-----TAILGFEAYAPDSVVGFKPY--QNLHLEFLRYSFMAALPA 188

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           +        + +L  + +  +  + PP++EQ DI N ++        + E   Q+I LL+
Sbjct: 189 LEQTSTQSTQANLNIDRIGAVKAVFPPLEEQLDIINYLDDMLYLYYSIEENTNQAIQLLQ 248

Query: 405 ERRSSFIAAAVTGQIDLR 422
           ERR++ I+AAVTG+ID+R
Sbjct: 249 ERRAALISAAVTGKIDVR 266



 Score = 43.1 bits (100), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 44/208 (21%), Positives = 88/208 (42%), Gaps = 14/208 (6%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK--------DIIYIGLEDVESGTGK 62
           KDSGV+W+G +P+HW +   +    +  G+     +        D  +I   DV   + K
Sbjct: 57  KDSGVEWLGEVPEHWSIKSYRYACLIYRGKFGHRPRNDPSLYDGDYPFIQTGDVARAS-K 115

Query: 63  YLPKDGNSRQSDTSTVS-IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVL 120
           ++     +       VS +F  G ++   +   +    I  F+       +  +P +++ 
Sbjct: 116 FIETYSQTLNEKGKAVSQLFPSGTLMMA-IAANIGDTAILGFEAYAPDSVVGFKPYQNLH 174

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            E L+   ++      +E     +T ++ +   IG +    PPL EQ+ I   +      
Sbjct: 175 LEFLRYSFMA--ALPALEQTSTQSTQANLNIDRIGAVKAVFPPLEEQLDIINYLDDMLYL 232

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVT 208
             ++     + I+LL+E++ AL+S  VT
Sbjct: 233 YYSIEENTNQAIQLLQERRAALISAAVT 260



 Score = 38.5 bits (88), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 28/39 (71%)

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           I + +  ETA+ID L+EK +Q I LLKE+R + I+ AVT
Sbjct: 9   IVSFLEHETAKIDNLIEKQQQLIELLKEKRQAVISHAVT 47


>gi|81299873|ref|YP_400081.1| type I restriction-modification [Synechococcus elongatus PCC 7942]
 gi|81168754|gb|ABB57094.1| type I restriction-modification [Synechococcus elongatus PCC 7942]
          Length = 453

 Score =  118 bits (296), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 131/252 (51%), Gaps = 17/252 (6%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTGRTSESGKDIIYIGLEDVESG--- 59
           +  YP YKD G++W+  +P HW V+ ++R   ++ +G +  +       G+  V      
Sbjct: 3   FPRYPAYKDCGIEWLEKLPSHWNVLQLRRLIPEIESGVSVNALDHAPDEGIPSVLKTSCV 62

Query: 60  -TGKYLPKDGNSR-QSDTSTVSIFAK-GQILYGKLG-PYLRKAI---IADFDGI-CSTQF 111
            TG + P++     Q D    +   K G+++  ++  P L  A    + D+D +    + 
Sbjct: 63  YTGSFRPEERKEIIQEDIDRAACPVKSGRLIVSRMNTPDLVGAAGLSLVDYDYVFLPDRL 122

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVL 169
             ++  +V P     W  +     +++ +C G  ++M +       +  +P+P   EQ+ 
Sbjct: 123 WQVRISNVYPNFAYYWTQTQIYRDQVKMVCSGTSSSMQNLSQDNFLSFILPVPSDEEQIA 182

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  ET +ID LI E+ R I LL+EK+QA++S+ VTKGLNPD  +KDSGIEW+G VP
Sbjct: 183 IASFLDRETAKIDALIAEQQRLIALLQEKRQAVISHAVTKGLNPDAPLKDSGIEWLGQVP 242

Query: 230 DHW---EVKPFF 238
            HW   ++K +F
Sbjct: 243 AHWKTGKIKHYF 254



 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 18/217 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           KDSG++W+G +P HWK   IK + K ++G T  + +  +Y    D +SG       D  +
Sbjct: 231 KDSGIEWLGQVPAHWKTGKIKHYFKTSSGGTPNTEEQALYYA--DSDSGIPWVRTTDIEN 288

Query: 71  RQSDTSTVSIFAKG---------------QILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           ++  ++ VSI  +                  LYG  G   +  I+  F    +     L 
Sbjct: 289 QEVRSAEVSITNQAIQDTACEILPVDTVLVALYGGGGTVGKNGILT-FPAAINQALCALL 347

Query: 116 PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           P      +     +       +E         +   + + +    +PPL EQ+LI + I 
Sbjct: 348 PSYYAVPMFTFRYIQFLRPFWMERAVSARKAGNISQELVRDTVFALPPLDEQILIVKHIH 407

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLN 212
           ++   I +L  E  + + LL+E++ AL+S  VT  ++
Sbjct: 408 SQLEEITSLENESTKSLSLLQERRSALISAAVTGQID 444



 Score = 50.8 bits (120), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 369 VPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           +PP+ EQ  I   I+ +   I  L  +  +S+ LL+ERRS+ I+AAVTGQID+RG
Sbjct: 393 LPPLDEQILIVKHIHSQLEEITSLENESTKSLSLLQERRSALISAAVTGQIDVRG 447



 Score = 42.4 bits (98), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 44/76 (57%)

Query: 341 DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
           D  K+  +  S   Q+L  ++     + VP  +EQ  I + ++ ETA+ID L+ + ++ I
Sbjct: 146 DQVKMVCSGTSSSMQNLSQDNFLSFILPVPSDEEQIAIASFLDRETAKIDALIAEQQRLI 205

Query: 401 VLLKERRSSFIAAAVT 416
            LL+E+R + I+ AVT
Sbjct: 206 ALLQEKRQAVISHAVT 221


>gi|226949372|ref|YP_002804463.1| restriction modification system DNA specificity domain protein
           [Clostridium botulinum A2 str. Kyoto]
 gi|226840941|gb|ACO83607.1| restriction modification system DNA specificity domain protein
           [Clostridium botulinum A2 str. Kyoto]
          Length = 450

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 121/456 (26%), Positives = 201/456 (44%), Gaps = 55/456 (12%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           KDSGV+WIG +   WK +P+K   K    + S     II      +  G G  L  +  +
Sbjct: 6   KDSGVEWIGYMNTCWKTMPLKFILKERRQKNSP----IITKERLSLSIGVGVTLYSEKTT 61

Query: 71  R----QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL---QPKDVLPEL 123
                + D +   +     ++   +   +    I+++ G  S  + V+    P+  + + 
Sbjct: 62  NLDRFKDDVTQYKVAYPNDLVINSMNVIVGAEGISNYLGCVSPAYYVMCSSNPQKFITKY 121

Query: 124 ----------------LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
                           L   +++ID  +     C     S+     +G +  P+P + EQ
Sbjct: 122 YDYCFKTSTIQKALFYLGKGIMAIDRGEGRVNTCRLKVSSY----DLGRLEFPVPSVNEQ 177

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I E +     +ID  I +  + IE LKE KQ++++  VTKGLNPDVKMKDSG+EW+G 
Sbjct: 178 HRIVEFLDNRCNKIDQTIQKEKQVIEKLKEYKQSVITEAVTKGLNPDVKMKDSGVEWIGE 237

Query: 228 VPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY---- 280
           +P HW+V   K  F+    L+     L+E  I  +SYG I  K    N+G+         
Sbjct: 238 IPKHWKVEKLKHIFSFKKGLSITKDNLVEEGIKVISYGQIHSK---SNIGVCINDSLIRY 294

Query: 281 --ETYQIVDPGEIVFR----FIDLQND-KRSLRSAQVMERGIITSAYMAVKPHGIDS--- 330
             E Y       +V R    F D   D + +     V +   I + Y  +    I     
Sbjct: 295 VGEEYLETGKQSLVLRNDFIFADTSEDLEGAGNYVYVGKNEEIFAGYHTIILTPIKDDIM 354

Query: 331 ---TYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVET 386
               Y A+L ++        +  SG++  S+  + +K+  V+VP IKEQ +IT+ ++ + 
Sbjct: 355 SEWKYFAYLYKTDCWRSQIRSRVSGIKLFSITQKILKQTEVIVPDIKEQKEITDYLDKKC 414

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           + ID L+   E+ I  L E + S I   VTG+ +++
Sbjct: 415 SSIDKLISDKEKVIKKLTEYKKSLIYECVTGKKEVQ 450



 Score = 73.2 bits (178), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 98/219 (44%), Gaps = 22/219 (10%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS--YGNIIQKLETRNM 273
           KMKDSG+EW+G +   W+  P   ++ E  +KN+ +I    LSLS   G  +   +T N+
Sbjct: 4   KMKDSGVEWIGYMNTCWKTMPLKFILKERRQKNSPIITKERLSLSIGVGVTLYSEKTTNL 63

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV---KPHGIDS 330
               +    Y++  P ++V   +++      + +      G ++ AY  +    P    +
Sbjct: 64  DRFKDDVTQYKVAYPNDLVINSMNVIVGAEGISNY----LGCVSPAYYVMCSSNPQKFIT 119

Query: 331 TYLAWLMRSYDLCKVFYAMGSGL-------------RQSLKFEDVKRLPVLVPPIKEQFD 377
            Y  +  ++  + K  + +G G+             R  +   D+ RL   VP + EQ  
Sbjct: 120 KYYDYCFKTSTIQKALFYLGKGIMAIDRGEGRVNTCRLKVSSYDLGRLEFPVPSVNEQHR 179

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           I   ++    +ID  ++K +Q I  LKE + S I  AVT
Sbjct: 180 IVEFLDNRCNKIDQTIQKEKQVIEKLKEYKQSVITEAVT 218


>gi|255744817|ref|ZP_05418767.1| hypothetical protein VCH_001143 [Vibrio cholera CIRS 101]
 gi|262161900|ref|ZP_06030918.1| hypothetical protein VIG_003073 [Vibrio cholerae INDRE 91/1]
 gi|255737288|gb|EET92683.1| hypothetical protein VCH_001143 [Vibrio cholera CIRS 101]
 gi|262028632|gb|EEY47287.1| hypothetical protein VIG_003073 [Vibrio cholerae INDRE 91/1]
          Length = 442

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 111/435 (25%), Positives = 205/435 (47%), Gaps = 28/435 (6%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTG--RTSESGKD-IIYIGLEDVESGTGK 62
           Y  YKDS  QWIG IP HW+V  +K    + + G   +  +G+D I+ + + D +    K
Sbjct: 8   YESYKDSCEQWIGDIPAHWEVYRLKSAVYECSNGIWGSDPNGRDEIVVLRVADFDDHKLK 67

Query: 63  YLPKDGNSRQ--SDTSTVSIFAKGQILYGKLG----PYLRKAIIAD--FDGICSTQFLVL 114
              +    R   +      +   G +L  K G      + + ++ D  +  + S     +
Sbjct: 68  ISDEKLTYRSIPAKEHQGRLLKNGDLLIEKSGGGDKTLVGRVVLFDKQYPAVTSNFVAKM 127

Query: 115 QPKDVLPELLQGWLLSIDVTQRIE--AICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
            PK+ +      ++ S      +   +I +   + + D     N    IP   EQ  I +
Sbjct: 128 TPKEWVISGFLKYVFSALYNNGVNYLSIKQTTGIQNLDASSYLNEKFCIPQKEEQYEIAK 187

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
            +  +T +I+  I  + + IELLKE+KQ ++   VT+GLNPD  MK SG++W+G +P HW
Sbjct: 188 FLDNKTTQINEAIAIKQKQIELLKERKQIIIQQAVTQGLNPDATMKYSGVDWIGAIPGHW 247

Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPGEI 291
            VK    L+ E+N ++   +E  +LS+S+   +     +N+ +   E Y   ++   G++
Sbjct: 248 IVKRAKYLLDEINERSETGLEE-LLSVSHMTGVTPRSEKNVTMFMAEDYTGSKLCHSGDL 306

Query: 292 VFRFIDLQNDKRSLRSAQVMER-GIITSAYMAVKPHGIDS---TYLAWLMRSYDLCKVFY 347
           V   +        + +  V +R GI++ +Y   +     +    YL  L++S    + + 
Sbjct: 307 VINIM-----WAWMGALGVSDRTGIVSPSYGVFREQREGTFVPKYLEMLLKSTKYVEYYN 361

Query: 348 AMGSGLRQS-LKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            + +GL  S L+F    +  + +  PP +EQ  I   I+ E +++D  +    + +  LK
Sbjct: 362 KVSTGLHSSRLRFYGHMLFDMALGFPPYEEQTQIVEYISRECSKVDEAITVQAEQVSKLK 421

Query: 405 ERRSSFIAAAVTGQI 419
           E +++ I +AVTG+I
Sbjct: 422 EYKTTLINSAVTGKI 436


>gi|153817790|ref|ZP_01970457.1| restriction modification system DNA specificity domain [Vibrio
           cholerae NCTC 8457]
 gi|262169768|ref|ZP_06037459.1| type I restriction-modification system specificity determinant
           [Vibrio cholerae RC27]
 gi|126511610|gb|EAZ74204.1| restriction modification system DNA specificity domain [Vibrio
           cholerae NCTC 8457]
 gi|262022002|gb|EEY40712.1| type I restriction-modification system specificity determinant
           [Vibrio cholerae RC27]
          Length = 442

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 114/446 (25%), Positives = 207/446 (46%), Gaps = 38/446 (8%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTG--RTSESGKD-IIYIGLEDV 56
           +K    Y  YKDS  QWIG IP HW+V  +K    + + G   +  +G+D I+ + + D 
Sbjct: 2   IKKMPKYESYKDSCEQWIGDIPAHWEVYRLKSAVYECSNGIWGSDPNGRDEIVVLRVADF 61

Query: 57  ESGTGK-------YLPKDGNSRQSDTSTVSIFAKGQILYGKLG----PYLRKAIIAD--F 103
           +    K       Y       RQ       +   G +L  K G      + + ++ D  +
Sbjct: 62  DDHKLKISDEKLTYRSIPAKERQG-----RLLKNGDLLIEKSGGGDKTLVGRVVLFDKQY 116

Query: 104 DGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIE--AICEGATMSHADWKGIGNIPMPI 161
             + S     + PK+ +      ++ S      +   +I +   + + D     N    I
Sbjct: 117 PAVTSNFVAKMTPKEWVISGFLKYVFSALYNNGVNYLSIKQTTGIQNLDASSYLNEKFCI 176

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           P   EQ  I + +  +T +I+  I  + + IELLKE+KQ ++   VT+GLNPD  MK SG
Sbjct: 177 PQKEEQYEIAKFLDNKTTQINEAIAIKQKQIELLKERKQIIIQQAVTQGLNPDATMKYSG 236

Query: 222 IEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESY 280
           ++W+G +P HW VK    L+ E+N ++   +E  +LS+S+   +     +N+ +   E Y
Sbjct: 237 VDWIGAIPGHWIVKRAKYLLDEINERSETGLEE-LLSVSHMTGVTPRSEKNVTMFMAEDY 295

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER-GIITSAYMAVKPHGIDS---TYLAWL 336
              ++   G++V   +        + +  V +R GI++ +Y   +     +    YL  L
Sbjct: 296 TGSKLCHSGDLVINIM-----WAWMGALGVSDRTGIVSPSYGVFREQREGTFVPKYLEML 350

Query: 337 MRSYDLCKVFYAMGSGLRQS-LKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
           ++S    + +  + +GL  S L+F    +  + +  PP +EQ  I   I+ E +++D  +
Sbjct: 351 LKSTKYVEYYNKVSTGLHSSRLRFYGHMLFDMALGFPPYEEQTQIVEYISRECSKVDEAI 410

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQI 419
               + +  LKE +++ I +AVTG+I
Sbjct: 411 TVQAEQVSKLKEYKTTLINSAVTGKI 436


>gi|15641771|ref|NP_231403.1| hypothetical protein VC1768 [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|153821172|ref|ZP_01973839.1| conserved hypothetical protein [Vibrio cholerae B33]
 gi|9656290|gb|AAF94917.1| conserved hypothetical protein [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|126521368|gb|EAZ78591.1| conserved hypothetical protein [Vibrio cholerae B33]
          Length = 462

 Score =  117 bits (294), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 111/435 (25%), Positives = 205/435 (47%), Gaps = 28/435 (6%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTG--RTSESGKD-IIYIGLEDVESGTGK 62
           Y  YKDS  QWIG IP HW+V  +K    + + G   +  +G+D I+ + + D +    K
Sbjct: 28  YESYKDSCEQWIGDIPAHWEVYRLKSAVYECSNGIWGSDPNGRDEIVVLRVADFDDHKLK 87

Query: 63  YLPKDGNSRQ--SDTSTVSIFAKGQILYGKLG----PYLRKAIIAD--FDGICSTQFLVL 114
              +    R   +      +   G +L  K G      + + ++ D  +  + S     +
Sbjct: 88  ISDEKLTYRSIPAKEHQGRLLKNGDLLIEKSGGGDKTLVGRVVLFDKQYPAVTSNFVAKM 147

Query: 115 QPKDVLPELLQGWLLSIDVTQRIE--AICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
            PK+ +      ++ S      +   +I +   + + D     N    IP   EQ  I +
Sbjct: 148 TPKEWVISGFLKYVFSALYNNGVNYLSIKQTTGIQNLDASSYLNEKFCIPQKEEQYEIAK 207

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
            +  +T +I+  I  + + IELLKE+KQ ++   VT+GLNPD  MK SG++W+G +P HW
Sbjct: 208 FLDNKTTQINEAIAIKQKQIELLKERKQIIIQQAVTQGLNPDATMKYSGVDWIGAIPGHW 267

Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPGEI 291
            VK    L+ E+N ++   +E  +LS+S+   +     +N+ +   E Y   ++   G++
Sbjct: 268 IVKRAKYLLDEINERSETGLE-ELLSVSHMTGVTPRSEKNVTMFMAEDYTGSKLCHSGDL 326

Query: 292 VFRFIDLQNDKRSLRSAQVMER-GIITSAYMAVKPHGIDS---TYLAWLMRSYDLCKVFY 347
           V   +        + +  V +R GI++ +Y   +     +    YL  L++S    + + 
Sbjct: 327 VINIM-----WAWMGALGVSDRTGIVSPSYGVFREQREGTFVPKYLEMLLKSTKYVEYYN 381

Query: 348 AMGSGLRQS-LKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            + +GL  S L+F    +  + +  PP +EQ  I   I+ E +++D  +    + +  LK
Sbjct: 382 KVSTGLHSSRLRFYGHMLFDMALGFPPYEEQTQIVEYISRECSKVDEAITVQAEQVSKLK 441

Query: 405 ERRSSFIAAAVTGQI 419
           E +++ I +AVTG+I
Sbjct: 442 EYKTTLINSAVTGKI 456


>gi|121585820|ref|ZP_01675614.1| conserved hypothetical protein [Vibrio cholerae 2740-80]
 gi|121727684|ref|ZP_01680779.1| conserved hypothetical protein [Vibrio cholerae V52]
 gi|147674628|ref|YP_001217309.1| hypothetical protein VC0395_A1366 [Vibrio cholerae O395]
 gi|153817792|ref|ZP_01970459.1| conserved hypothetical protein [Vibrio cholerae NCTC 8457]
 gi|227081913|ref|YP_002810464.1| hypothetical protein VCM66_1706 [Vibrio cholerae M66-2]
 gi|298498162|ref|ZP_07007969.1| conserved hypothetical protein [Vibrio cholerae MAK 757]
 gi|121549958|gb|EAX59976.1| conserved hypothetical protein [Vibrio cholerae 2740-80]
 gi|121629981|gb|EAX62389.1| conserved hypothetical protein [Vibrio cholerae V52]
 gi|126511612|gb|EAZ74206.1| conserved hypothetical protein [Vibrio cholerae NCTC 8457]
 gi|146316511|gb|ABQ21050.1| conserved hypothetical protein [Vibrio cholerae O395]
 gi|227009801|gb|ACP06013.1| conserved hypothetical protein [Vibrio cholerae M66-2]
 gi|227013668|gb|ACP09878.1| conserved hypothetical protein [Vibrio cholerae O395]
 gi|297542495|gb|EFH78545.1| conserved hypothetical protein [Vibrio cholerae MAK 757]
          Length = 462

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 114/446 (25%), Positives = 207/446 (46%), Gaps = 38/446 (8%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTG--RTSESGKD-IIYIGLEDV 56
           +K    Y  YKDS  QWIG IP HW+V  +K    + + G   +  +G+D I+ + + D 
Sbjct: 22  IKKMPKYESYKDSCEQWIGDIPAHWEVYRLKSAVYECSNGIWGSDPNGRDEIVVLRVADF 81

Query: 57  ESGTGK-------YLPKDGNSRQSDTSTVSIFAKGQILYGKLG----PYLRKAIIAD--F 103
           +    K       Y       RQ       +   G +L  K G      + + ++ D  +
Sbjct: 82  DDHKLKISDEKLTYRSIPAKERQG-----RLLKNGDLLIEKSGGGDKTLVGRVVLFDKQY 136

Query: 104 DGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIE--AICEGATMSHADWKGIGNIPMPI 161
             + S     + PK+ +      ++ S      +   +I +   + + D     N    I
Sbjct: 137 PAVTSNFVAKMTPKEWVISGFLKYVFSALYNNGVNYLSIKQTTGIQNLDASSYLNEKFCI 196

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           P   EQ  I + +  +T +I+  I  + + IELLKE+KQ ++   VT+GLNPD  MK SG
Sbjct: 197 PQKEEQYEIAKFLDNKTTQINEAIAIKQKQIELLKERKQIIIQQAVTQGLNPDATMKYSG 256

Query: 222 IEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESY 280
           ++W+G +P HW VK    L+ E+N ++   +E  +LS+S+   +     +N+ +   E Y
Sbjct: 257 VDWIGAIPGHWIVKRAKYLLDEINERSETGLE-ELLSVSHMTGVTPRSEKNVTMFMAEDY 315

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER-GIITSAYMAVKPHGIDS---TYLAWL 336
              ++   G++V   +        + +  V +R GI++ +Y   +     +    YL  L
Sbjct: 316 TGSKLCHSGDLVINIM-----WAWMGALGVSDRTGIVSPSYGVFREQREGTFVPKYLEML 370

Query: 337 MRSYDLCKVFYAMGSGLRQS-LKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
           ++S    + +  + +GL  S L+F    +  + +  PP +EQ  I   I+ E +++D  +
Sbjct: 371 LKSTKYVEYYNKVSTGLHSSRLRFYGHMLFDMALGFPPYEEQTQIVEYISRECSKVDEAI 430

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQI 419
               + +  LKE +++ I +AVTG+I
Sbjct: 431 TVQAEQVSKLKEYKTTLINSAVTGKI 456


>gi|54308077|ref|YP_129097.1| type I restriction-modification system specificity determinant
           [Photobacterium profundum SS9]
 gi|46912503|emb|CAG19295.1| hypothetical type I restriction-modification system specificity
           determinant [Photobacterium profundum SS9]
          Length = 437

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 114/437 (26%), Positives = 193/437 (44%), Gaps = 36/437 (8%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG-----LEDVESGTG 61
           Y  Y +SGV+WIG IP+HW +   K        R+    ++++ +          E    
Sbjct: 10  YEAYNESGVEWIGNIPEHWNITKAKYLFNEVDERSVTGHEELLSVSHITGVTPRSEKNVS 69

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
            ++ +D +  ++  +   +F       G LG   R  I++   G+   +F        L 
Sbjct: 70  MFMAEDYSGSKTCQADDIVFNTMWAWMGALGVSERSGIVSPSYGVFRQKFTNTFNAKYLE 129

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAEQVLIREKIIAETV 179
            LL+    +    +    +  G   S   + G    ++ M  P + EQ  I + +  +T 
Sbjct: 130 YLLK----TPKYIEHYNKVSTGLHSSRLRFYGHMFFDMKMGYPHIDEQNGIIKFLDNKTN 185

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF-F 238
           +ID     + + I LLKE+KQ ++   VT+GLNPDV M+DSG++W+G +PDHW  +P  +
Sbjct: 186 KIDEAAAIKEKQISLLKERKQIIIQQAVTRGLNPDVPMRDSGVDWIGEIPDHWCSEPIKY 245

Query: 239 AL--VTELNRKNTKLIE-SNILSLSYGNIIQ-KL------ETRNMGLKPESYETYQIVDP 288
           +L  + +   K    ++      +   N+ Q KL       T   G K   + +  +  P
Sbjct: 246 SLKGIIDCEHKTAPFVDKKEFFVVRTSNVKQGKLVIEDAKYTNEYGYK--EWTSRGVPFP 303

Query: 289 GEIVFRF------IDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDL 342
           G+I+           L  D R L   Q M    +    +   P    S   + ++R+Y  
Sbjct: 304 GDILLTREAPAGEACLVPDDRKLCLGQRMVWLKVDRTRLL--PEFALSLIYSSVVRTY-- 359

Query: 343 CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
              F + GS +       D+K +PV++PPI EQ  +   I   + +ID  +E  +Q I  
Sbjct: 360 -IDFLSAGSTVLH-FNMADIKNIPVILPPINEQAILVTHIKKHSDKIDKAIELEQQQISK 417

Query: 403 LKERRSSFIAAAVTGQI 419
           LKE +S  I +AVTG+I
Sbjct: 418 LKEYKSILINSAVTGKI 434


>gi|300825349|ref|ZP_07105428.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300522184|gb|EFK43253.1| conserved hypothetical protein [Escherichia coli MS 119-7]
          Length = 441

 Score =  117 bits (293), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 111/440 (25%), Positives = 208/440 (47%), Gaps = 34/440 (7%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIK---RFTKLNTGRTSESGKDIIYIGLE-----DVES 58
           Y  YKDSGV+W+G IP  W ++  K   R  K   G+ S S  D++ + L      D+E+
Sbjct: 10  YEVYKDSGVEWLGDIPASWSLLANKHIFRLKKKQVGKRS-SEYDLLSLTLRGVIKRDMEN 68

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
             GK+ P + ++ Q       IF    +   +  P  R   ++ F+G+ +  + V +  D
Sbjct: 69  PEGKF-PAEFDTYQEVQCGDFIFCLFDV---EETP--RTVGLSPFNGMITGAYTVFELND 122

Query: 119 VLPE-LLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
                 L  + +++D  + ++ +  G   T+    +         +PP  +Q  I   + 
Sbjct: 123 NFDNRFLYYFYMNLDAKKMLKPLYRGLRNTIPKDSFLSFKTF---VPPHEQQTRIANFLD 179

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
            +   ID  I+ + + I LLKE KQ ++   VT+GL+P+V MKDSG++W+G +P+HWEV 
Sbjct: 180 KKIALIDEAISIKEKQINLLKEHKQIIIQQAVTQGLDPNVPMKDSGVDWIGDIPEHWEVV 239

Query: 236 PFFAL------VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPG 289
           P   L      V   NRK+ +L+    L++   +    ++   +    +  + + + + G
Sbjct: 240 PLKRLAVLSPSVKVSNRKSKELV--TFLAMEKVSTDGFIDQDTLMPICDVSQGFTVFNRG 297

Query: 290 EIVFRFID--LQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVF 346
           +++   I    +N K +  +    E G  ++ +  ++    I  ++L  ++ S       
Sbjct: 298 DVIVAKITPCFENGKSAWLNNLQTEFGYGSTEFHVLRCGQRIIGSFLYLIVSSPLFLNAG 357

Query: 347 YAM--GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            AM  GS  ++ +    ++  P  +P + EQ  I + +    ++IDV+V      I  LK
Sbjct: 358 EAMMTGSAGQKRVPSSFIQNFPTAIPGVAEQEKIVSKVKELFSQIDVVVASTVNQIEKLK 417

Query: 405 ERRSSFIAAAVTGQIDLRGE 424
           E +++ I +AVTG+I +  E
Sbjct: 418 EYKTTLINSAVTGKIKITPE 437


>gi|289706815|ref|ZP_06503158.1| type I restriction modification DNA specificity domain protein
           [Micrococcus luteus SK58]
 gi|289556500|gb|EFD49848.1| type I restriction modification DNA specificity domain protein
           [Micrococcus luteus SK58]
          Length = 410

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 107/370 (28%), Positives = 167/370 (45%), Gaps = 42/370 (11%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWL-LSIDVTQRIEA 139
           F  G +L+ KL PYL K+ +A+ DG       V +P D +     G+L LS    +++ A
Sbjct: 56  FRAGDLLFSKLRPYLAKSWVANRDGEALGDIHVYRPVDEMCSRYLGYLVLSSFFLEQVNA 115

Query: 140 ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKK 199
              G  M  A+W  I  I +  P    Q  I + +  ET  ID LI ++   + LL +++
Sbjct: 116 STYGTRMPRANWDFIKTIEVWAPDFDTQRRIADYLDRETATIDALIEKQRALLTLLIDRR 175

Query: 200 QALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSL 259
            ++  ++  +G      M  +  EW G +P HW   P  + V  L   +T     +   L
Sbjct: 176 ASVRKHLALRGPESRTSMVQAPEEWAGQIPSHWRFVPLLS-VARLGSGHTP--SKSRPEL 232

Query: 260 SYGNIIQKLETRNMGLKPES---YETY-------------QIVDPGEIVFRFIDLQNDKR 303
                I  +  R++G    +   YET+             +I+  G +V     L  D  
Sbjct: 233 WTDTTIPWISLRDVGSMRATTYLYETHTSISELGLASSSARILPAGTVV-----LSRDAT 287

Query: 304 SLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAM---------GSGLR 354
             R+A +M R + TS + A    G        L+  Y    +  AM         GS LR
Sbjct: 288 IGRTA-IMGRDMATSQHFAAWTCGPQ------LLPQYLHLVLADAMQDHLESLTDGSTLR 340

Query: 355 QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAA 414
            ++   D++ L V +PP+ EQ  I +    ETA+ID L+ K E+ I L +ERR++ I AA
Sbjct: 341 -TVGMGDIRALRVPLPPVHEQRRIIDESETETAKIDALIAKAERFIELAQERRAALITAA 399

Query: 415 VTGQIDLRGE 424
           VTGQI++  E
Sbjct: 400 VTGQIEIPSE 409



 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 105/219 (47%), Gaps = 22/219 (10%)

Query: 8   PQYKDSGVQ----WIGAIPKHWKVVPIKRFTKLNTGRTSESGK-------DIIYIGLEDV 56
           P+ + S VQ    W G IP HW+ VP+    +L +G T    +        I +I L DV
Sbjct: 187 PESRTSMVQAPEEWAGQIPSHWRFVPLLSVARLGSGHTPSKSRPELWTDTTIPWISLRDV 246

Query: 57  ESGTGKYLPKDGNSRQSD----TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
            S        + ++  S+    +S+  I   G ++  +     R AI+   D   S  F 
Sbjct: 247 GSMRATTYLYETHTSISELGLASSSARILPAGTVVLSRDATIGRTAIMGR-DMATSQHFA 305

Query: 113 V--LQPKDVLPELLQGWLLSIDVTQ-RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
                P+ +LP+ L   L+  D  Q  +E++ +G+T+       I  + +P+PP+ EQ  
Sbjct: 306 AWTCGPQ-LLPQYLH--LVLADAMQDHLESLTDGSTLRTVGMGDIRALRVPLPPVHEQRR 362

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           I ++   ET +ID LI +  RFIEL +E++ AL++  VT
Sbjct: 363 IIDESETETAKIDALIAKAERFIELAQERRAALITAAVT 401


>gi|229819988|ref|YP_002881514.1| restriction modification system DNA specificity domain protein
           [Beutenbergia cavernae DSM 12333]
 gi|229565901|gb|ACQ79752.1| restriction modification system DNA specificity domain protein
           [Beutenbergia cavernae DSM 12333]
          Length = 427

 Score =  117 bits (292), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 124/411 (30%), Positives = 194/411 (47%), Gaps = 57/411 (13%)

Query: 47  DIIYIGLEDVESGTGKYLPKDGNSRQSDTST-----VSIFAKGQILYGKL-GPYLRKAII 100
           DI  + L DV  G GK+  KD + R  +  T      S    G IL  ++  P  R  ++
Sbjct: 32  DIRLLQLADV--GDGKF--KDKSDRWINEETFRRLRCSWVHPGDILIARMPDPLGRACVV 87

Query: 101 ADFDG--ICSTQFLVLQPKDVLPELLQGWLL-----SIDVTQRIEAICEGATMSHADWKG 153
            +  G  I      VL+P    P+      L     S      +E   +GAT      K 
Sbjct: 88  PEGLGKTITVVDVAVLRPD---PDQADAGYLTYAINSAKTRSEVERQQDGATRQRIPRKR 144

Query: 154 IGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNP 213
           +G + +P+PPL EQ  I + + AET +ID LI E+ R I LLKE++ + +   VT+GL  
Sbjct: 145 LGRVSIPLPPLEEQRRIADFLDAETTQIDALIAEQERLIGLLKERRASGILQAVTRGLR- 203

Query: 214 DVKMKDSGIEWVGLVPDHWEV---KPFFALVT--ELNRKNTKL-IESNILSLSYGNIIQK 267
           DV +K S + WV  VP HW V   + F A+ T    +R N +  ++++I   +  ++ Q 
Sbjct: 204 DVDLKPSTLTWVDAVPLHWTVANIRRFAAMKTGHTPSRSNPEYWVDTHIPWFTLADVWQV 263

Query: 268 LETR------------NMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGI 315
            + R            ++GL   + E   ++  G +V       +   S+  + VM R +
Sbjct: 264 RDGRRTHLGETENTISDLGLANSAAE---LLPAGTVVL------SRTASVGFSGVMPRPM 314

Query: 316 ITSA--YMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVK---RLPVLVP 370
            TS   +  V    +   YL +L R+  +   F A+  G      ++ V    R+P  VP
Sbjct: 315 ATSQDFWNWVCGPELVPEYLMYLFRA--MRGEFNALMIGSTHKTIYQPVAAAIRVP--VP 370

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           P++EQ +I   I+  T + D L+ + E +I L KERR++ I AAVTGQID+
Sbjct: 371 PLEEQHEIVARIDERTRKTDALINEAEHNIALSKERRAALITAAVTGQIDV 421



 Score = 56.6 bits (135), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 92/219 (42%), Gaps = 31/219 (14%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-SESGKD------IIYIGLED---VESGT 60
           K S + W+ A+P HW V  I+RF  + TG T S S  +      I +  L D   V  G 
Sbjct: 208 KPSTLTWVDAVPLHWTVANIRRFAAMKTGHTPSRSNPEYWVDTHIPWFTLADVWQVRDGR 267

Query: 61  GKYLPKDGNSRQSD----TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
             +L +  N+  SD     S   +   G ++       L +     F G+        Q 
Sbjct: 268 RTHLGETENT-ISDLGLANSAAELLPAGTVV-------LSRTASVGFSGVMPRPMATSQ- 318

Query: 117 KDVL-----PELLQGWLLSIDVTQRIE--AICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
            D       PEL+  +L+ +    R E  A+  G+T           I +P+PPL EQ  
Sbjct: 319 -DFWNWVCGPELVPEYLMYLFRAMRGEFNALMIGSTHKTIYQPVAAAIRVPVPPLEEQHE 377

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           I  +I   T + D LI E    I L KE++ AL++  VT
Sbjct: 378 IVARIDERTRKTDALINEAEHNIALSKERRAALITAAVT 416


>gi|330874481|gb|EGH08630.1| type I restriction-modification system specificity subunit
           [Pseudomonas syringae pv. morsprunorum str. M302280PT]
          Length = 421

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 117/413 (28%), Positives = 197/413 (47%), Gaps = 40/413 (9%)

Query: 23  KHWKVVPIKRFTKLNTGRTSES---GKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           K W++  +K    +N   +      G+   ++ +E V S  G+    +    ++  S  +
Sbjct: 23  KKWRICRLKHVALINPYLSLSRVRWGEPATFLPMEAV-STDGQVDYSEPEDSKNLVSGFT 81

Query: 80  IFAKGQILYGKLGPYL---RKAIIADFD---GICSTQFLVLQ-PKDVLPELLQGWLLSID 132
            F  G ++  K+ P     + A+++D     G  ST+F VL+  K  +P  +     S  
Sbjct: 82  NFEAGDVILAKITPCFENGKGAVLSDMPTRVGFGSTEFHVLRVNKKAIPNFIYYITKSDL 141

Query: 133 VTQRIEAICEG-ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
             ++ EA+  G A         + N  + +P L EQ  I + +  +T  I   I+++   
Sbjct: 142 FMRQGEALMIGSAGQKRVSTSYVENFQLALPSLHEQRKIVDFLEEKTSLIAEAISKKEYQ 201

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV---KPFFALVTELNRKN 248
           IELL+E+KQ LV   VT+GL+P   M+++GIEW+G +P HWEV   K  F    EL RKN
Sbjct: 202 IELLEERKQILVQQAVTRGLDPAAPMRNAGIEWIGEIPKHWEVRRSKFTFNQRKELARKN 261

Query: 249 TKLIESNILSLSYGNIIQKLETRNMGLKPE----SYETYQIVDPGEIVFRFIDLQNDKRS 304
              + +   + SYG I Q      +G K      + E  + V+ G+ V           S
Sbjct: 262 DIQLSA---TQSYGVIPQDEYEEKVGRKVVKILFNLEKRKHVEVGDFVI----------S 308

Query: 305 LRSAQ-VMER----GIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFYAMGSGLR--QS 356
           +RS Q  +ER    G I S+Y+ +KP  GID  Y ++L++S        A  + +R  Q 
Sbjct: 309 MRSFQGGLERAWASGCIRSSYVILKPLPGIDPGYYSYLLKSKRYIAALQATANFIRDGQD 368

Query: 357 LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSS 409
           L FE+   + + +PP+ EQ +I   +    ++ D  +  +EQ I+ LKE +++
Sbjct: 369 LNFENFALVDLPIPPLDEQKEIARYLASWLSKADRGLYLLEQQIIKLKEYKAT 421


>gi|295135948|ref|YP_003586624.1| type I restriction-modification system specificity determinant
           [Zunongwangia profunda SM-A87]
 gi|294983963|gb|ADF54428.1| type I restriction-modification system specificity determinant
           [Zunongwangia profunda SM-A87]
          Length = 350

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 94/340 (27%), Positives = 164/340 (48%), Gaps = 32/340 (9%)

Query: 100 IADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNI 157
           +++ DG  S   +V++P D+       +L S    +    I  G  A +    +  + NI
Sbjct: 20  VSESDGSVSLINIVMEPNDIFGSFCNYFLKSKAFVEENYRIGHGIVADLWTTRYDEMKNI 79

Query: 158 PMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKM 217
            M  PP  EQ  I   +     ++DT++ ++ + I LLKE+KQAL+   VT+GLN +V M
Sbjct: 80  IMAFPPKPEQQAIANFLDETCEKLDTVVAQKEKMIALLKERKQALIQNAVTRGLNKNVPM 139

Query: 218 KDSGIEWVGLVPDHWEVK--PFFALVTE------LNRKN--------TKLIESNILSLSY 261
           KDSG++W+G +P +WEVK   F  ++ +      LN+K         +   E  ILS  Y
Sbjct: 140 KDSGVDWIGEIPKNWEVKRLKFICVLNKESLPENLNKKQEINYVDIGSVTFEDGILSTEY 199

Query: 262 GNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM 321
             + Q   +R    +  +     IV       + ID  ++ +S        + + ++ + 
Sbjct: 200 Y-LFQNAPSR---ARKVAKNGDTIVSTVRTYLKAIDFIDENKS--------KYVYSTGFA 247

Query: 322 AVKPH-GIDSTYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDIT 379
            + P+  I + YL   +R+    +       G+   ++   D+ R+ V VP  +EQ  I 
Sbjct: 248 ILSPNKNILNKYLYNQVRADAFTEQVSYNSKGMSYPAINSTDLGRIWVCVPSKQEQEKIV 307

Query: 380 NVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           N I+ ++ ++D  V + EQ+IV LKE ++S I + V G+I
Sbjct: 308 NYIDAQSRKLDQAVTQQEQAIVKLKEYKASLIDSCVLGKI 347



 Score = 62.8 bits (151), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 57/209 (27%), Positives = 95/209 (45%), Gaps = 17/209 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK--------DIIYIGLEDVESGTGK 62
           KDSGV WIG IPK+W+V  +K    LN     E+          DI  +  ED    T  
Sbjct: 140 KDSGVDWIGEIPKNWEVKRLKFICVLNKESLPENLNKKQEINYVDIGSVTFEDGILSTEY 199

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG---ICSTQFLVLQP-KD 118
           YL ++  SR        +   G  +   +  YL+     D +    + ST F +L P K+
Sbjct: 200 YLFQNAPSRAR-----KVAKNGDTIVSTVRTYLKAIDFIDENKSKYVYSTGFAILSPNKN 254

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           +L + L   + +   T+++    +G +    +   +G I + +P   EQ  I   I A++
Sbjct: 255 ILNKYLYNQVRADAFTEQVSYNSKGMSYPAINSTDLGRIWVCVPSKQEQEKIVNYIDAQS 314

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIV 207
            ++D  +T++ + I  LKE K +L+   V
Sbjct: 315 RKLDQAVTQQEQAIVKLKEYKASLIDSCV 343


>gi|325297666|ref|YP_004257583.1| restriction modification system DNA specificity domain [Bacteroides
           salanitronis DSM 18170]
 gi|324317219|gb|ADY35110.1| restriction modification system DNA specificity domain [Bacteroides
           salanitronis DSM 18170]
          Length = 429

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 121/442 (27%), Positives = 191/442 (43%), Gaps = 49/442 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESG----------KDIIYIGLEDV 56
           Y +YKDSGVQW+G IP HW+V   KR     T R  +            K+ IY  LE+V
Sbjct: 5   YSEYKDSGVQWLGKIPSHWEV---KRLASCFTERKVKVSDKEFDPLSVTKNGIYPQLENV 61

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
                     DG++R+   S   +        G  G       +A  DG  S   +VL+P
Sbjct: 62  AKTN------DGDNRKLVLSGDFVINSRSDRKGSSG-------VAKQDGSVSLINIVLKP 108

Query: 117 -KDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
            K++ P+     L      +       G  A +    +  +  I + +P L EQ  I   
Sbjct: 109 RKNIYPDFCNYLLKCYSFIEEYYRNGRGIVADLWTTRYDEMKTIKISVPLLNEQKAIVRY 168

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +   T +ID  I ++ + I+LL E+KQ +++  VTKGLNPDV MK+SG+EW+G +P HW 
Sbjct: 169 LNKVTSKIDEAIAQQQKMIDLLNERKQIIINNAVTKGLNPDVPMKNSGVEWIGKIPKHWT 228

Query: 234 VKPFFALVTELNR------KNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
                       R      K+ + +++    LS  NI+      N   K      ++  +
Sbjct: 229 TIRLGYCAWIRARLGWKGLKSDEYVDNGYPFLSAFNIVNNKLDWN---KLNYINKFRYEE 285

Query: 288 PGEIVFRFID--LQNDKRSL-RSAQV--MERGIITSAYMAVKPHGIDSTYLAWLM----- 337
             EI  R  D  L  D   + + A+V  +  G  T+          +  Y  +L      
Sbjct: 286 SPEIKLRIGDILLVKDGAGIGKCARVDSLPLGEATANGSLAFITANERVYYKFLHYYIIS 345

Query: 338 RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            S++  K     G G+    + E +K + + +PP+ EQ+ I   ++     ID ++E   
Sbjct: 346 NSFNKYKDLLITGMGVPHLTQGE-IKNMMLPIPPLNEQYIIVQRLDKNINVIDNILEHYL 404

Query: 398 QSIVLLKERRSSFIAAAVTGQI 419
           Q I  L+ER+   I   VTG++
Sbjct: 405 QQITFLQERKRIIINDVVTGKV 426


>gi|50086399|ref|YP_047909.1| putative type I restriction-modification system specificity
           determinant for hsdM and hsdR (HsdS) [Acinetobacter sp.
           ADP1]
 gi|49532375|emb|CAG70087.1| putative type I restriction-modification system specificity
           determinant for hsdM and hsdR (HsdS) [Acinetobacter sp.
           ADP1]
          Length = 448

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 120/458 (26%), Positives = 212/458 (46%), Gaps = 49/458 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRF--TKL----NTGRTSESGKDIIYIGLE 54
           M     Y  YK+SGVQW+G IP HW+V  +K     KL    N    SE      YI + 
Sbjct: 1   MSQLPCYESYKNSGVQWLGEIPSHWEVKRMKFLLSEKLKYGANESAESEDKDQPRYIRIT 60

Query: 55  DV-ESGTGKYLPKDG-NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGI---CST 109
           D+ +SGT   L +D   S + + +   +     IL  + G  + K+ +   D +   C  
Sbjct: 61  DINDSGT---LREDTFKSLEIEKAQEYLLNDLDILLARSGATVGKSYLHKKDKVNVACYA 117

Query: 110 QFLV---LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
            +L+      ++  P+ +  +L S      IE++   AT+ +   +   ++ + IP LAE
Sbjct: 118 GYLIRARFNKENYDPQFINLFLQSKAYWSWIESVNIQATIQNVSAEKYNDLALSIPSLAE 177

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q +I + +     ++D LI ++   +E L E++ AL+S+ VTKGLNPDV+MK+S +  +G
Sbjct: 178 QKIIADFLDKRLAQVDALIAKQETLLEKLAEQRVALISHAVTKGLNPDVEMKESDVVLLG 237

Query: 227 LVPDHWEVKPF-FALVTELNRKNTKLIES-NILSLSYGNIIQKLETRNMGLKPESYETYQ 284
            +P+ W +K   F L  +L     +  ES +  +  Y  I    ++ N  LK E++++ +
Sbjct: 238 NIPNTWNIKRLKFLLSEKLKYGANESAESEDKENPRYIRITDIDDSGN--LKDETFKSLE 295

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRS----- 339
                E    ++    D    RS   + +  +  A    +  GI + Y  +L+R+     
Sbjct: 296 ----SEKAQEYLLDDLDILLARSGATVGKSYLYKA----ESVGI-ACYAGYLIRARLDQE 346

Query: 340 -YDLCKVFYAMGS-------------GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
            Y+   V Y + S                Q++  E    L + +P ++EQ  +   +  E
Sbjct: 347 NYNPEFVNYFLQSKQYWDWISSINIQATIQNVSAEKYNDLTLAIPSLEEQKQLIEYLKNE 406

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
             + +  + K ++ + LL E RS+ I   VTG+ID++ 
Sbjct: 407 DEKFNRAISKGKKLVHLLNEYRSTLITQVVTGKIDVQN 444


>gi|170731314|ref|YP_001776747.1| putative type I restriction enzyme, S subunit [Xylella fastidiosa
           M12]
 gi|167966107|gb|ACA13117.1| putative type I restriction enzyme, S subunit [Xylella fastidiosa
           M12]
          Length = 457

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 70/200 (35%), Positives = 108/200 (54%), Gaps = 4/200 (2%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           K SG++W+G +P +W+V  +K      T +T+   +D IY+ +E V+S TG   P +G  
Sbjct: 219 KPSGIEWLGDVPVNWEVRRLKFLASNTTSQTTTKARDEIYLAMEHVQSWTGVARPLEGEV 278

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWL 128
             +  STV  F    +L+GKL PYL K   A  +G+C ++FLVL+ +   +LP  L+  L
Sbjct: 279 EFA--STVKRFVVDDVLFGKLRPYLAKVTRAKCNGVCVSEFLVLRSRKEFILPAYLEQML 336

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITER 188
               V   I +   GA M  ADW  IGN+ +P+P    Q  I   I +ET  +   IT  
Sbjct: 337 RCKRVIDLINSSTAGAKMPRADWIFIGNVRLPVPCKDVQEAILSHIESETKDLGEAITRT 396

Query: 189 IRFIELLKEKKQALVSYIVT 208
              I+L++E +  L++ +VT
Sbjct: 397 EDEIKLIREYRDRLITDVVT 416



 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 113/447 (25%), Positives = 186/447 (41%), Gaps = 48/447 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M     Y  Y+    +W+  +P+HW ++  K F +    R S++G++ +           
Sbjct: 1   MAVASTYSTYQPLRSRWVPRVPEHWSLLRAKNFLQEIDDR-SKTGEETLL--------SM 51

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGP---YLRKAIIAD-------FDGICSTQ 110
            K+    G    +D S      K  I Y K+ P    L +    +         G+ S  
Sbjct: 52  RKHC---GLVPHNDVSIKRTNPKNLIGYKKVQPDELVLNRMQAGNAMFFHNYLSGLVSPD 108

Query: 111 FLVLQP-KDVLPELLQGWLLS---IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
           + V +  +D  PE L G+L     I    R E+   G       W     + +P+PPL E
Sbjct: 109 YAVFRLLRDDNPEYL-GYLFRSWPICGLFRSESKGIGTGFLRLYWDRFAALEIPLPPLPE 167

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q  I   + A+ V I   I  +   I LL E+K  ++ + VT+GL+  V +K SGIEW+G
Sbjct: 168 QDQIVAYLRAQDVHIARFIKAKRDLISLLIEQKLRIIDHAVTRGLDASVALKPSGIEWLG 227

Query: 227 LVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIV 286
            VP +WEV+    L +    + T      I        ++ +++     +P   E    V
Sbjct: 228 DVPVNWEVRRLKFLASNTTSQTTTKARDEIYL-----AMEHVQSWTGVARPLEGE----V 278

Query: 287 DPGEIVFRFI--DLQNDKRSLRSAQVME---RGIITSAYMAVKPHG--IDSTYLAWLMRS 339
           +    V RF+  D+   K     A+V      G+  S ++ ++     I   YL  ++R 
Sbjct: 279 EFASTVKRFVVDDVLFGKLRPYLAKVTRAKCNGVCVSEFLVLRSRKEFILPAYLEQMLRC 338

Query: 340 YDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
             +  +  +  +G    R    F    RLPV    ++E   I + I  ET  +   + + 
Sbjct: 339 KRVIDLINSSTAGAKMPRADWIFIGNVRLPVPCKDVQEA--ILSHIESETKDLGEAITRT 396

Query: 397 EQSIVLLKERRSSFIAAAVTGQIDLRG 423
           E  I L++E R   I   VTGQ+D+RG
Sbjct: 397 EDEIKLIREYRDRLITDVVTGQVDVRG 423


>gi|150399018|ref|YP_001322785.1| restriction modification system DNA specificity subunit
           [Methanococcus vannielii SB]
 gi|150011721|gb|ABR54173.1| restriction modification system DNA specificity domain
           [Methanococcus vannielii SB]
          Length = 407

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 105/424 (24%), Positives = 185/424 (43%), Gaps = 42/424 (9%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTS-----ESGKDIIYIGLEDVESGTGKYLP 65
           KDSG++WIG IP  W V+  K    ++TG        + G    +I  ++VE        
Sbjct: 6   KDSGIEWIGDIPADWNVIKTKHLCDISTGNQDTINRVDGGDYPFFIRSKNVERINTYSFD 65

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQ 125
            +      D     IF     + GK   + R    +DF  +    F      +++ EL +
Sbjct: 66  GEAVLTAGDGDVGKIF---HYIDGKFDYHQRVYKFSDFRSVIGRYFYYYISSNLIRELGK 122

Query: 126 GWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
                 +    +E++          W  +   P+ +  + EQ  I + +  +  +ID++I
Sbjct: 123 -----YNAKTTVESL-------RLPW--LKEFPVIVSKIEEQQQIAQYLDDKVGQIDSII 168

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN 245
            +    IE  K+ KQ++++  VTKGL+P V MKDSG+EW+G +P+HW++    +L+ E+N
Sbjct: 169 EKTKSSIEEYKKYKQSIMTETVTKGLDPTVMMKDSGVEWIGDIPEHWDMVKIKSLLYEIN 228

Query: 246 RKNTKLIESNILSLSYGN---IIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDK 302
            +N   ++ N + LS      +  + E    G K  +   Y+IV  G+++       N  
Sbjct: 229 ERN---VDENAVLLSLFTALGVAPRSEMEEKGNKAVTVINYKIVKRGDLIV------NKL 279

Query: 303 RSLRSAQVME--RGIITSAYMAVKPHGID---STYLAWLMRSYDLCKVFYAMGSG---LR 354
            +   A       G+ +  Y   + H      + +  W  R        Y  G G   +R
Sbjct: 280 LAWMGAIAFSDYEGVTSPDYDVYRFHENAEALTEFYEWYFRFTKFKDDCYKFGRGIMMMR 339

Query: 355 QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAA 414
                   K + V+ PP++EQ  I + +  + A ID L++K ++ I  L+  + S I   
Sbjct: 340 WRTYPAQFKNIYVVNPPLEEQKQIIDYLKQKIADIDQLIDKKQRLITELESYKKSLIYEV 399

Query: 415 VTGQ 418
           VTG+
Sbjct: 400 VTGK 403


>gi|124485664|ref|YP_001030280.1| hypothetical protein Mlab_0842 [Methanocorpusculum labreanum Z]
 gi|124363205|gb|ABN07013.1| restriction modification system DNA specificity domain
           [Methanocorpusculum labreanum Z]
          Length = 446

 Score =  114 bits (285), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 106/429 (24%), Positives = 192/429 (44%), Gaps = 29/429 (6%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K Y +Y D+G  WI  +PK W+  PI   T L+  R  +  KD+  + +   E G  K  
Sbjct: 3   KGYEEYMDTGYDWIPQVPKTWEQRPIHSITTLSNERNGKR-KDLELLSVYR-EFGVIKKS 60

Query: 65  PKDGNSR--QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ-PKDVLP 121
            +D N      D S       G ++  K+  +     I+ ++GI S  ++V +  +D++ 
Sbjct: 61  SRDDNHNVESQDLSNYKYVNSGYLVMNKMKMWQGSLGISQYEGIVSPAYIVCKVDQDIIG 120

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHAD--WKGIGNIPMPIPPLAEQVLIREKIIAETV 179
           + L   L S         I  G  +   D  +  + N+ + +P   EQ  I   + A+  
Sbjct: 121 KYLHYLLRSSHFKIFYNRISYGVRVGQWDLRYNDLKNLKIYLPTSDEQNQIVRYLNAKVA 180

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
           +I+ LI+ + + I LLKE KQA+++  VTKG+   V MK+SG+EW+G +P+ WE +    
Sbjct: 181 KINRLISAKKKEIALLKEYKQAIITRAVTKGICAGVPMKESGVEWIGEIPEGWEERKLKY 240

Query: 240 LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE-----IVFR 294
           L + +N  +   I  N   L Y   ++  +  +  +   S++   ++  G+      VF 
Sbjct: 241 LCS-INTGDKDTINRNDDGL-YPFYVRSPKIEH--IDTYSFDGEAVLMAGDGVGAGKVFH 296

Query: 295 FIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLR 354
           ++  + D           + +    Y       +   Y+ + ++     K+  A      
Sbjct: 297 YVSGKFD---------YHQRVYNLHYFK----DVCGKYIYYYLKENFWRKIEEASAKSTV 343

Query: 355 QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAA 414
            S++   +   PV+   I EQ  I + ++ + + ID  ++K E +I  L     S I   
Sbjct: 344 DSVRLPMLLEFPVVFGQIGEQQQIVSYLDAKCSAIDATIQKRELAIEKLTAYNQSLIYEC 403

Query: 415 VTGQIDLRG 423
           VTG++D+RG
Sbjct: 404 VTGKVDVRG 412


>gi|228964022|ref|ZP_04125152.1| hypothetical protein bthur0004_8820 [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228795674|gb|EEM43151.1| hypothetical protein bthur0004_8820 [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 409

 Score =  114 bits (285), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 111/400 (27%), Positives = 184/400 (46%), Gaps = 35/400 (8%)

Query: 47  DIIYIGLEDVESGTGKYLPKDGNSRQSDTS------TVSIFAKGQILYGKLGPYLRKAII 100
           DI +I +ED     GKY+  D  SRQ  +        + +F  G +L       +    I
Sbjct: 15  DIPWIRIEDF---NGKYI-SDSKSRQYVSKELVKGMNLKVFPIGTVLC-TCSCSMGATAI 69

Query: 101 ADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
            +   I +  F+ + P + L      +L+     +R++   +GA   +       ++ +P
Sbjct: 70  VEQPLISNQTFIGIVPGENLDSEYLFYLMQAS-AERLQLFAQGAIQQYLSKHNFEHLKIP 128

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           +P L  Q  +   +  +   +D LI  + + I+LL+EK+Q L++  VT+GLNP+VKMKDS
Sbjct: 129 LPSLKIQKRLLVFLNRKLKDLDELIENKKQLIDLLEEKRQTLITEAVTRGLNPNVKMKDS 188

Query: 221 GIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK---- 276
           G+EW+G +P+HW +K    +   +    T    S I   S    ++ +     G++    
Sbjct: 189 GVEWIGEIPEHWTIKKIKHISNLVGSGKTPKGGSEIYPESGVLFLRSMNVHYDGIRLKDI 248

Query: 277 ----PESYETYQI--VDPGEIVFRFIDLQNDK-----RSLRSAQVMER-GIITSAYMAVK 324
               PE  E  +   V   +++         +      SL  A V +   II S    V 
Sbjct: 249 VHITPEIDEDMRSTRVKSKDVLLNITGASIGRSCIVPESLGKANVNQHVCIIRSNTKVVV 308

Query: 325 PHGIDSTYLAWLMRS-YDLCKVFYAMGSGLRQSLKFEDVKRLPV-LVPPIKEQFDITNVI 382
           P       L+ +M S + + ++  +     R+ L F  VK L   L   ++EQ +I N I
Sbjct: 309 PE-----LLSKIMASNFIMQQILMSQNGSSREGLNFTQVKNLEFPLTRDLQEQIEIANHI 363

Query: 383 NVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           +VET +I+ L+  IE+ I  LKE R S I   VTG+ID+R
Sbjct: 364 SVETNKINSLIGMIEEQIQKLKEYRQSLIYEVVTGKIDVR 403



 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 100/217 (46%), Gaps = 20/217 (9%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKL-NTGRTSESGKDII-YIGLEDVESGTGKYLPK 66
           + KDSGV+WIG IP+HW +  IK  + L  +G+T + G +I    G+  + S    Y   
Sbjct: 184 KMKDSGVEWIGEIPEHWTIKKIKHISNLVGSGKTPKGGSEIYPESGVLFLRSMNVHY--- 240

Query: 67  DGNSRQ----------SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL-- 114
           DG   +           D  +  + +K  +L        R  I+ +  G  +    V   
Sbjct: 241 DGIRLKDIVHITPEIDEDMRSTRVKSKDVLLNITGASIGRSCIVPESLGKANVNQHVCII 300

Query: 115 --QPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP-PLAEQVLIR 171
               K V+PELL   + S  + Q+I     G++    ++  + N+  P+   L EQ+ I 
Sbjct: 301 RSNTKVVVPELLSKIMASNFIMQQILMSQNGSSREGLNFTQVKNLEFPLTRDLQEQIEIA 360

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             I  ET +I++LI      I+ LKE +Q+L+  +VT
Sbjct: 361 NHISVETNKINSLIGMIEEQIQKLKEYRQSLIYEVVT 397


>gi|15597930|ref|NP_251424.1| hypothetical protein PA2734 [Pseudomonas aeruginosa PAO1]
 gi|9948811|gb|AAG06122.1|AE004701_5 hypothetical protein PA2734 [Pseudomonas aeruginosa PAO1]
          Length = 431

 Score =  114 bits (284), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 72/200 (36%), Positives = 102/200 (51%), Gaps = 4/200 (2%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           K S ++W+G +P HW+V  +K      T +T+    D IY+ LE V+S TG   P  G  
Sbjct: 193 KPSDIEWLGEVPAHWEVKRLKFLAGNITSQTTTKADDEIYLALEHVQSWTGVARPLGGEV 252

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWL 128
             +  STV  F    +L+GKL PYL K       G+C ++FLVL+ +   +LP  L+  L
Sbjct: 253 EFA--STVKRFVADDVLFGKLRPYLAKVTRVVCAGVCVSEFLVLRSRQELILPAYLEQLL 310

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITER 188
               V   I +   GA M  ADW  IGN+ +PIP   EQ  I   I  ET  +D  I   
Sbjct: 311 RCKRVIDLISSSTAGAKMPRADWNFIGNVRLPIPRKDEQEAILSHIGRETKDLDETIARA 370

Query: 189 IRFIELLKEKKQALVSYIVT 208
              I+L++E +  L++  VT
Sbjct: 371 EDEIKLIREYRDRLIADAVT 390



 Score =  100 bits (248), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 95/350 (27%), Positives = 154/350 (44%), Gaps = 16/350 (4%)

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLL-SIDVTQRIEAIC 141
           KG I Y  +  +         DG+ S  ++V++P          +L  +    Q +    
Sbjct: 55  KGDIAYNMMRMWQGAVGPVPEDGLVSPAYVVVKPYAEANSTYFSYLFRTAAYMQEVNKFS 114

Query: 142 EG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKK 199
            G  A  +   W+    +P  +PP  EQ  I   +  +   I   I  +   I LL E+K
Sbjct: 115 RGIVADRNRLYWESFKQMPSLVPPRPEQDQIVTYLRTQDAHIACFIRAKRDLIALLTEQK 174

Query: 200 QALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNI-LS 258
             ++ + VT+GL+  VK+K S IEW+G VP HWEVK    L   +  + T   +  I L+
Sbjct: 175 LRIIDHAVTRGLDASVKLKPSDIEWLGEVPAHWEVKRLKFLAGNITSQTTTKADDEIYLA 234

Query: 259 LSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITS 318
           L +      +  R +G + E   T +     +++F  +     K +    +V+  G+  S
Sbjct: 235 LEHVQSWTGV-ARPLGGEVEFASTVKRFVADDVLFGKLRPYLAKVT----RVVCAGVCVS 289

Query: 319 AYMAVKPHG--IDSTYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIK 373
            ++ ++     I   YL  L+R   +  +  +  +G    R    F    RLP  +P   
Sbjct: 290 EFLVLRSRQELILPAYLEQLLRCKRVIDLISSSTAGAKMPRADWNFIGNVRLP--IPRKD 347

Query: 374 EQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           EQ  I + I  ET  +D  + + E  I L++E R   IA AVTGQ+DLRG
Sbjct: 348 EQEAILSHIGRETKDLDETIARAEDEIKLIREYRDRLIADAVTGQVDLRG 397


>gi|91225110|ref|ZP_01260332.1| hypothetical type I restriction-modification system specificity
           determinant [Vibrio alginolyticus 12G01]
 gi|91190053|gb|EAS76324.1| hypothetical type I restriction-modification system specificity
           determinant [Vibrio alginolyticus 12G01]
          Length = 464

 Score =  114 bits (284), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 125/248 (50%), Gaps = 25/248 (10%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRF--TKLNTGRTSESGKDII----YIGLEDVE 57
           Y+AYP+YKDS V+W+  IPK W    +K    + ++ G    + + +     YI + D+ 
Sbjct: 10  YQAYPEYKDSDVEWLDDIPKDWCTRRLKHMLESPMSYGANEAAERAVSTEPRYIRITDMN 69

Query: 58  SG------TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII--ADFDGICST 109
           S       T + LPKD        ++  +     IL  + G  + K+ I   +F   C  
Sbjct: 70  SDGTLKEDTFRSLPKD-------IASDYLLKDRDILLARSGATVGKSFIYRKEFGDCCFA 122

Query: 110 QFLVLQPKDV--LPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP-LA 165
            +L+    D   L      W   S    Q I      AT+ +   +  G + + +P  + 
Sbjct: 123 GYLIKVSCDSARLNSDYAFWFFQSSSYWQYISGSQIQATIQNVSAEKYGEMYISLPEHVE 182

Query: 166 EQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           EQ  I   +  ET +IDTLI ++ + I+LLKEK+QA++S+ VTKGLNP   MK+SG+EW+
Sbjct: 183 EQTQIANFLDHETAKIDTLIEKQQQLIKLLKEKRQAVISHAVTKGLNPQAPMKNSGVEWL 242

Query: 226 GLVPDHWE 233
           G VP+HWE
Sbjct: 243 GEVPEHWE 250



 Score = 70.1 bits (170), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 94/209 (44%), Gaps = 12/209 (5%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKL---NTGRTSESGKDIIYIGLEDVESGTGKYLPKD 67
           K+SGV+W+G +P+HW+ + +K  T        +T+    D  Y+         GK L  D
Sbjct: 235 KNSGVEWLGEVPEHWEQIKLKHITHQIVDAEHKTAPYFDDGEYLVCRTTNVRDGK-LRLD 293

Query: 68  GNSRQSDTSTVSIFAKGQ-----ILYGKLGPYLRKAIIADFDGICSTQFLVL---QPKDV 119
           G    +         +GQ     IL+ +  P     +      +C  Q +VL       V
Sbjct: 294 GGKYTNHAIYEEWTKRGQPEVGDILFTREAPAGEACVYTGEVPLCLGQRMVLFKLNQTRV 353

Query: 120 LPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
           LPE +   + S      ++ + +G+T++H +   I NIP+  PP  EQ  I + +     
Sbjct: 354 LPEFVLHSIYSGLADDFVKQLSQGSTVAHFNMSDIQNIPLFEPPKDEQAQIVDHLAKVLA 413

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVT 208
           + D L +     IEL++E++ AL+S  VT
Sbjct: 414 KYDALTSSASLKIELMQERRTALISAAVT 442



 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/93 (35%), Positives = 54/93 (58%), Gaps = 6/93 (6%)

Query: 328 IDSTYLAWLMRSYDLCKVFYAMGSGLR---QSLKFEDVKRLPVLVPP-IKEQFDITNVIN 383
           ++S Y  W  +S    +  Y  GS ++   Q++  E    + + +P  ++EQ  I N ++
Sbjct: 135 LNSDYAFWFFQSSSYWQ--YISGSQIQATIQNVSAEKYGEMYISLPEHVEEQTQIANFLD 192

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
            ETA+ID L+EK +Q I LLKE+R + I+ AVT
Sbjct: 193 HETAKIDTLIEKQQQLIKLLKEKRQAVISHAVT 225



 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 38/67 (56%)

Query: 357 LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
               D++ +P+  PP  EQ  I + +    A+ D L       I L++ERR++ I+AAVT
Sbjct: 383 FNMSDIQNIPLFEPPKDEQAQIVDHLAKVLAKYDALTSSASLKIELMQERRTALISAAVT 442

Query: 417 GQIDLRG 423
           G+ID+R 
Sbjct: 443 GKIDVRN 449


>gi|220933784|ref|YP_002512683.1| type I restriction-modification system, S subunit [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219995094|gb|ACL71696.1| type I restriction-modification system, S subunit [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 458

 Score =  112 bits (281), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 82/254 (32%), Positives = 121/254 (47%), Gaps = 29/254 (11%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M  Y+AYP+Y+++    +  IP HW    IK    +  G+  +S          D ++  
Sbjct: 1   MGKYQAYPEYRETRHDLLPPIPVHWMTGQIKNAHDVVLGKMLQS----------DAKTPA 50

Query: 61  GKYLP----KDGNSRQSDTSTVS--IFAK----------GQILYGKLGPYLRKAIIADFD 104
            + LP     + N    D STV    F+           G ++  + G   R A+     
Sbjct: 51  DRLLPYLRAANVNWGGVDLSTVKEMWFSPAERKALRLMVGDVVISEGGDVGRSAVWQGEL 110

Query: 105 GICSTQFLV--LQPK-DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPI 161
             C  Q  +   +PK +     L  W+  I     I+ IC  +T+ H   + +   P   
Sbjct: 111 PECYFQNAINRARPKGEHSSRYLYYWMSFIKSAGYIDIICNKSTIPHYTAEKVQGTPFLF 170

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG 221
           PP  EQ  I   +  ET +ID LI ++ R IELLKEK+QA++S+ VTKGLNPD  MKDSG
Sbjct: 171 PPAGEQAGIAAFLDHETAKIDRLIAKQQRLIELLKEKRQAVISHAVTKGLNPDAPMKDSG 230

Query: 222 IEWVGLVPDHWEVK 235
           +EW+G VP HW ++
Sbjct: 231 VEWLGEVPAHWRLE 244



 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 97/211 (45%), Gaps = 16/211 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES------GKDIIYIGLEDVESGTGKYL 64
           KDSGV+W+G +P HW++  +K       G T         G DI ++  +D++S   +Y+
Sbjct: 227 KDSGVEWLGEVPAHWRLEKLKYTAIFKGGGTPSKDSPEYWGGDIPWVSPKDMKS---RYV 283

Query: 65  PKDGNSRQSD---TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--- 118
               +    +    S+ S+   GQ+L       L++ I    + +  T    ++  D   
Sbjct: 284 ADSQDKITVEAIAASSTSLIGPGQVLVVVRSGILQRTIPVAVNLVEVTLNQDMKAIDFRD 343

Query: 119 -VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
               E    ++   +    +E   +GAT+   + + +GN  +P+PP +E + I + +  +
Sbjct: 344 ETRSEFFSYFVEGHEDNLLLEWRKQGATVESIEQEYLGNTMVPMPPPSEMMEILQFLNGQ 403

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             +   L  +  R IELL+E + AL+S  VT
Sbjct: 404 LEKYRLLTEKATRAIELLREHRTALISAAVT 434



 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 44/69 (63%)

Query: 355 QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAA 414
           +S++ E +    V +PP  E  +I   +N +  +  +L EK  ++I LL+E R++ I+AA
Sbjct: 373 ESIEQEYLGNTMVPMPPPSEMMEILQFLNGQLEKYRLLTEKATRAIELLREHRTALISAA 432

Query: 415 VTGQIDLRG 423
           VTG+ID+RG
Sbjct: 433 VTGKIDVRG 441



 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%)

Query: 360 EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           E V+  P L PP  EQ  I   ++ ETA+ID L+ K ++ I LLKE+R + I+ AVT
Sbjct: 161 EKVQGTPFLFPPAGEQAGIAAFLDHETAKIDRLIAKQQRLIELLKEKRQAVISHAVT 217


>gi|217979675|ref|YP_002363822.1| hypothetical protein Msil_3571 [Methylocella silvestris BL2]
 gi|217505051|gb|ACK52460.1| conserved hypothetical protein [Methylocella silvestris BL2]
          Length = 458

 Score =  112 bits (280), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 111/446 (24%), Positives = 192/446 (43%), Gaps = 53/446 (11%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYI----GLEDVESGT 60
           + Y     +G+ W+G +P HW V  IK   +    R+    + ++ +    GL D     
Sbjct: 6   RPYADTNPTGLPWLGDVPAHWNVRRIKTLLREVDSRSKTGEERLLSLRMRQGLVDHIDAG 65

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
           GK +P +            I   GQ++  ++        +A+  G+ S  + V +P   L
Sbjct: 66  GKLIPPE------SLVNFKIVEPGQVVMNRMRAAAGLFGVANVRGLVSPDYAVFEP---L 116

Query: 121 PELLQGWLL------SIDVTQRIEAICEGATMS-----HADWKGIGNIPMPIPPLAEQVL 169
           PE    +LL      S+    R E+   G   S     + D    G IP+P PPL EQ L
Sbjct: 117 PEAFNPYLLQAFRLPSLSAVFRAESKGLGTGESGFLRLYTD--RFGPIPVPYPPLDEQRL 174

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +     +   LI  + + I LL E+KQA++   VT+GL+P+V++K SGI W+G +P
Sbjct: 175 IVRFLDWHGAQTAKLIRAKKKIIALLNEQKQAIIHRAVTRGLDPNVRLKPSGIPWLGDIP 234

Query: 230 DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDP- 288
           + WEV         LN +   L          G    ++  R      + Y    ++D  
Sbjct: 235 EDWEVSRVKTEFQCLNYRRVPL---------SGTERGRMTVRQY----DYYGASGVIDKV 281

Query: 289 GEIVF--RFIDLQNDK-----RSLRSAQVMERGIITSAYMAV-KPHGIDSTYLAWLMRSY 340
            E +F  + + +  D      R+L  A + E     + +  + KP   D  +LA ++   
Sbjct: 282 DEFLFDDKLLLIAEDGANLVLRNLPLAIIAEGKFWVNNHAHILKPRRGDIRFLAAILEGL 341

Query: 341 DLCKVFYAMGSGLRQSLKFED-VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           +    F    SG  Q    +D +  + + VPP  +Q +I    + E + +   +    + 
Sbjct: 342 N----FLPWISGAAQPKLTQDRLMGIAIAVPPGHKQLEIIQSCDEEVSELVRAINVASKE 397

Query: 400 IVLLKERRSSFIAAAVTGQIDLRGES 425
           ++ ++E R+  IA  VTG++D+R  +
Sbjct: 398 LIFIQEFRTRLIADVVTGKLDVRAAA 423



 Score = 70.9 bits (172), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 105/226 (46%), Gaps = 27/226 (11%)

Query: 210 GLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSY-GNIIQKL 268
           GL P      +G+ W+G VP HW V+    L+ E++ + +K  E  +LSL     ++  +
Sbjct: 4   GLRPYADTNPTGLPWLGDVPAHWNVRRIKTLLREVDSR-SKTGEERLLSLRMRQGLVDHI 62

Query: 269 ETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVM-----ERGIITSAYMAV 323
           +     + PES   ++IV+PG++V            +R+A  +      RG+++  Y   
Sbjct: 63  DAGGKLIPPESLVNFKIVEPGQVVM---------NRMRAAAGLFGVANVRGLVSPDYAVF 113

Query: 324 KPHGIDSTYLAWLMRSY---DLCKVFYAMGSGLRQS------LKFEDVKRLPVLVPPIKE 374
           +P  +   +  +L++++    L  VF A   GL         L  +    +PV  PP+ E
Sbjct: 114 EP--LPEAFNPYLLQAFRLPSLSAVFRAESKGLGTGESGFLRLYTDRFGPIPVPYPPLDE 171

Query: 375 QFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           Q  I   ++   A+   L+   ++ I LL E++ + I  AVT  +D
Sbjct: 172 QRLIVRFLDWHGAQTAKLIRAKKKIIALLNEQKQAIIHRAVTRGLD 217


>gi|331007189|ref|ZP_08330402.1| Type I restriction-modification system, specificity subunit S
           [gamma proteobacterium IMCC1989]
 gi|330419021|gb|EGG93474.1| Type I restriction-modification system, specificity subunit S
           [gamma proteobacterium IMCC1989]
          Length = 288

 Score =  112 bits (280), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/274 (29%), Positives = 134/274 (48%), Gaps = 7/274 (2%)

Query: 151 WKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKG 210
           +  I N  + +PP  EQV I   +  +T +ID  I  + + I LLKE+KQ ++   VT+G
Sbjct: 14  FNHIANSLLILPPETEQVAIANFLDQKTAQIDEAIAIKEKQIALLKERKQIIIQKAVTQG 73

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           LNPDV MKDSG++W+G +PDHW VK    ++ E N ++    E   +      ++ + + 
Sbjct: 74  LNPDVPMKDSGVDWIGQIPDHWGVKRLKYVLDERNERSKTGEEPLFMVSQVHGLVVRADY 133

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA--VKPHGI 328
            +      S    ++V   ++VF    L+        + +   G+++  Y     K H  
Sbjct: 134 HDKAEVAASNIDNKVVYKNDLVFN--KLKAHLGVFFKSNIEFEGLVSPDYAVYKCKAHIA 191

Query: 329 DSTYLAWLMRSYDLCKVFYAMGSGLRQS---LKFEDVKRLPVLVPPIKEQFDITNVINVE 385
           D  YL  L R     + F    +G+ +    L   D+  +PV + P  EQ +I   I  +
Sbjct: 192 DVKYLELLFRHSSYIEQFIIRATGIVEGLIRLYTGDLFDIPVPIAPENEQLEILAYIEKQ 251

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           +   D  V+  ++ I  LKE +++ I +AVTG+I
Sbjct: 252 SKTFDRAVDLQQRQIQKLKEYKTTLINSAVTGKI 285



 Score = 53.1 bits (126), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 42/68 (61%)

Query: 349 MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRS 408
           +GSG+RQ++ F  +    +++PP  EQ  I N ++ +TA+ID  +   E+ I LLKER+ 
Sbjct: 4   LGSGVRQTISFNHIANSLLILPPETEQVAIANFLDQKTAQIDEAIAIKEKQIALLKERKQ 63

Query: 409 SFIAAAVT 416
             I  AVT
Sbjct: 64  IIIQKAVT 71



 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 56/208 (26%), Positives = 94/208 (45%), Gaps = 16/208 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           KDSGV WIG IP HW V  +K        R S++G++ +++ +  V     +    D   
Sbjct: 81  KDSGVDWIGQIPDHWGVKRLKYVLDERNER-SKTGEEPLFM-VSQVHGLVVRADYHDKAE 138

Query: 71  RQSDTSTVSIFAKGQILYGK----LGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
             +      +  K  +++ K    LG + +  I  +F+G+ S  + V + K  + ++   
Sbjct: 139 VAASNIDNKVVYKNDLVFNKLKAHLGVFFKSNI--EFEGLVSPDYAVYKCKAHIADVKYL 196

Query: 127 WLL---SIDVTQ---RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            LL   S  + Q   R   I EG    +     + +IP+PI P  EQ+ I   I  ++  
Sbjct: 197 ELLFRHSSYIEQFIIRATGIVEGLIRLYTG--DLFDIPVPIAPENEQLEILAYIEKQSKT 254

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVT 208
            D  +  + R I+ LKE K  L++  VT
Sbjct: 255 FDRAVDLQQRQIQKLKEYKTTLINSAVT 282


>gi|293115630|ref|ZP_05792396.2| putative type I restriction-modification system [Butyrivibrio
           crossotus DSM 2876]
 gi|292809171|gb|EFF68376.1| putative type I restriction-modification system [Butyrivibrio
           crossotus DSM 2876]
          Length = 441

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 113/440 (25%), Positives = 209/440 (47%), Gaps = 40/440 (9%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVES---GTGKYLP 65
           + KDSG++W+G IP++WKV        L      E  K+II  G + VE+      KY  
Sbjct: 16  EMKDSGIEWVGKIPENWKV--------LKNKYNFELSKEII--GTKWVETQLLSLTKYGV 65

Query: 66  K---DGNSRQSDTSTVSIFAKGQ-----ILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
           K   DG        ++S + K       +    L      + I++FDG+ S  +  ++ K
Sbjct: 66  KAINDGEQTGKVPESLSTYQKVNKDDIVMCLFDLDCSAVFSGISNFDGMISPAYKCIRCK 125

Query: 118 -DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
             + P+ +  +  ++ V ++ +   +    S +  + + N+P+ +PP+  Q  I E +  
Sbjct: 126 PHLCPQYVDYYFRTVFVDRKYKRYSKNVRFSISSDEFM-NLPIIVPPIDIQKKIAEFLNF 184

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           +   IDTL ++  + I+ L+E K+++++  VTKGL+PDV+MKDSGI ++G +P HW+V  
Sbjct: 185 KCFEIDTLHSDIEKQIKTLEEYKKSIITEAVTKGLDPDVEMKDSGISYIGNIPKHWKVTN 244

Query: 237 FFALVTELN--RKNTKLIESNILSLSYGNII------QKLETRNMGLKPESYETYQIVDP 288
              L    N   K  +   +    +SYG++       Q ++   M  K E  +    V  
Sbjct: 245 LKYLGKCQNGISKGGEYFGNGFPFVSYGDVYKNYSIPQNVDGLIMSTKTE--QNIYSVKY 302

Query: 289 GEIVFRFIDLQNDKRSLRSA--QVMERGIITSAYMAVKPHGID--STYLAWLMRSYDLCK 344
           G++ F       ++    S   + ++  +     +  +P   D    +  +  RS ++ +
Sbjct: 303 GDVFFTRTSETIEEIGFASTCLKSIDNSVFAGFLIRFRPTSSDLIPEFSKFYFRS-NIHR 361

Query: 345 VFYAMGSGL--RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
            F+     L  R SL    + RLPVL+PP+ EQ  I   +  + A ID  +E+ ++ +  
Sbjct: 362 KFFVKEMNLVTRASLSQNLLGRLPVLLPPLCEQQMIAKNLEKKCAEIDGAIEEKKEQLET 421

Query: 403 LKERRSSFIAAAVTGQIDLR 422
           L++ + S I   VTG+ +++
Sbjct: 422 LEQYKKSLIYEYVTGKKEVK 441


>gi|222444442|ref|ZP_03606957.1| hypothetical protein METSMIALI_00053 [Methanobrevibacter smithii
           DSM 2375]
 gi|222434007|gb|EEE41172.1| hypothetical protein METSMIALI_00053 [Methanobrevibacter smithii
           DSM 2375]
          Length = 245

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 129/247 (52%), Gaps = 33/247 (13%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKR------------FTKLNTGRTSESGKDIIYI 51
           ++   ++KDS V++IG IPK WK++  K             + K N    +++G     +
Sbjct: 2   FRYNNEFKDSKVEYIGKIPKSWKIIRNKHIFNKTKVIAGPNWDKYNILSLTKNG-----V 56

Query: 52  GLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA--DFDGICST 109
            ++D+E   GK +P       SD S   I   G +L   L   +    +   + +GI S 
Sbjct: 57  IIKDIERNEGK-MP-------SDFSIYQIVNPGNLLMCLLDIDVTPRCVGYIENNGIVSA 108

Query: 110 QFLVLQP-KDVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAE 166
            +  L P  D+  +    W L +D+ +++  + +    ++S  D+  +  +    PPL E
Sbjct: 109 AYTELSPIADINMKYYYWWYLMLDIDKQLLHLSKNLRNSLSTEDFMALSVVK---PPLDE 165

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
           Q+ I   +  +T +ID  I +    I+LL+EK+ AL++++VTKGL+PDV MKDSGIEW+G
Sbjct: 166 QIQIANYLNKKTAKIDETIAKNKELIDLLEEKRIALINHVVTKGLDPDVPMKDSGIEWIG 225

Query: 227 LVPDHWE 233
            +P+HWE
Sbjct: 226 NIPEHWE 232



 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 68/209 (32%), Positives = 106/209 (50%), Gaps = 8/209 (3%)

Query: 216 KMKDSGIEWVGLVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRN 272
           + KDS +E++G +P  W++   K  F     +   N    + NILSL+   +I K   RN
Sbjct: 7   EFKDSKVEYIGKIPKSWKIIRNKHIFNKTKVIAGPNWD--KYNILSLTKNGVIIKDIERN 64

Query: 273 MGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDST 331
            G  P  +  YQIV+PG ++   +D+    R +    +   GI+++AY  + P   I+  
Sbjct: 65  EGKMPSDFSIYQIVNPGNLLMCLLDIDVTPRCV--GYIENNGIVSAAYTELSPIADINMK 122

Query: 332 YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
           Y  W     D+ K    +   LR SL  ED   L V+ PP+ EQ  I N +N +TA+ID 
Sbjct: 123 YYYWWYLMLDIDKQLLHLSKNLRNSLSTEDFMALSVVKPPLDEQIQIANYLNKKTAKIDE 182

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            + K ++ I LL+E+R + I   VT  +D
Sbjct: 183 TIAKNKELIDLLEEKRIALINHVVTKGLD 211



 Score = 38.5 bits (88), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 19/24 (79%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFT 34
           KDSG++WIG IP+HW+ + +K  T
Sbjct: 217 KDSGIEWIGNIPEHWETIKLKNCT 240


>gi|86738913|ref|YP_479313.1| type I restriction-modification system specificity determinant
           [Frankia sp. CcI3]
 gi|86565775|gb|ABD09584.1| type I restriction-modification system specificity determinant
           [Frankia sp. CcI3]
          Length = 416

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 107/431 (24%), Positives = 184/431 (42%), Gaps = 45/431 (10%)

Query: 12  DSGVQWIGAIPKHWKVVPI-KRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           DSGV W+G +P HW   P+   F ++      E     ++     V   +   + K   +
Sbjct: 10  DSGVSWLGKVPPHWTTKPLWSMFERIKDVDHPEEQMLSVFREYGVVAKDSRDNINKTAEN 69

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLL- 129
           R    S   +   G ++  ++  +     I+   GI S  ++   P+         WLL 
Sbjct: 70  R----SIYQLVHPGWLVANRMKAWQGSVGISSLRGIVSGHYICFAPRHSEDARYLNWLLR 125

Query: 130 SIDVTQRIEAICEGATMSHADWKGIGN-----IPMPIPPLAEQVLIREKIIAETVRIDTL 184
           S   T     +  G  +  A+   I N     +P+ +PPL EQ  I + +  ET RIDTL
Sbjct: 126 STTYTNGYALLSRGVRIGQAE---IDNDEFRLMPILLPPLGEQRAIADYLDRETARIDTL 182

Query: 185 ITERIRFIELLKEKKQALVSYIVTKGLNPDV---KMKDSGIEWVGLVP-----DHWEVKP 236
           I E+ R IE+L+E+++A+  + + + ++      K+  S     G  P      +W    
Sbjct: 183 IEEQQRLIEMLRERRRAVALHAIDQQIHAGATTDKLGRSTRIGNGSTPRRETASYWRDGE 242

Query: 237 FFAL-VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETY-QIVDPGEIVFR 294
           F  L  + +N       +  +  ++                   YE +  +V PG ++  
Sbjct: 243 FPWLNSSAVNESRVTHADQFVTDIAL------------------YECHLPVVAPGSVLVG 284

Query: 295 FIDLQNDKRSLRSAQVMERGIITS-AYMAVKPHGIDSTYLAWLMR-SYDLCKVFYAMGSG 352
               Q   R + +   +E  +    AY+A         YL W +R SYD  +        
Sbjct: 285 LTG-QGKTRGMATLLEIEATVNQHVAYIAPDRGTWLPEYLLWSLRASYDDLRRLSEENGS 343

Query: 353 LRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIA 412
            +  L  + +K+  + VPP+ EQ  +   ++ +TA+ID L+ + E+ I L +ERR + I 
Sbjct: 344 TKGGLTCQALKQYRLAVPPLDEQRRVAAYLDEQTAKIDSLIGETERFIELARERRVALIT 403

Query: 413 AAVTGQIDLRG 423
           AAVTGQ+D+RG
Sbjct: 404 AAVTGQVDVRG 414


>gi|53802449|ref|YP_112811.1| hypothetical protein MCA0277 [Methylococcus capsulatus str. Bath]
 gi|53756210|gb|AAU90501.1| conserved hypothetical protein [Methylococcus capsulatus str. Bath]
          Length = 474

 Score =  111 bits (277), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 109/453 (24%), Positives = 202/453 (44%), Gaps = 55/453 (12%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           YP Y+ +  +W+  +P+HW ++  K F +    R+    + ++ + ++            
Sbjct: 7   YPNYQPTRSRWVPRVPEHWSLLRAKNFLREIDDRSKTGEETLLSMRMQR----------- 55

Query: 67  DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
            G    +D S   I  +  I Y K+ P   + ++       +  F   Q   V P+    
Sbjct: 56  -GLVPHNDVSVKRIAPENLIGYKKVQP--NELVLNRMQAGNAMFFRSRQSGLVSPDYAVF 112

Query: 127 WLLSIDVTQRIEAICEGATMS---HADWKGIG---------------NIPMPIPPLAEQV 168
            LL  D  + +  +     M     ++ KG+G               ++ +P+PP  EQ 
Sbjct: 113 RLLRDDNPEYLGHLFRSWPMRGLFRSESKGLGTGTSGFLRLYSDRFASLEIPLPPRPEQD 172

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I   + A+   I   I  +   I+LL E+K  ++ + VT+GL+P+V++K SGI+W+G V
Sbjct: 173 QIVAYLRAQDAHIARYILAKRELIKLLTEQKLTIIDHAVTRGLDPNVRLKPSGIQWLGEV 232

Query: 229 PDHWEVKPF-------FALVTELNRKNTKLIESNILSLSYGNIIQKLE-TRNMGLKPESY 280
           P+HWEV          F+ V     K++   E+ +   +Y ++ +    T +M L   + 
Sbjct: 233 PEHWEVASIKHIADVRFSGVD----KHSNDDETPVRLCNYTDVYKNERITADMDLMRATA 288

Query: 281 ETYQI----VDPGEIVFRFIDLQNDKRSLRSAQVMER--GIITSAYMAV---KPHGIDST 331
              +I    +  G+++        D   +  A V E   G++ + ++ +    P  +   
Sbjct: 289 TAAEIARLTLKAGDVILTKDSETPDDIGV-PAWVPEDLPGVVCAYHLGLLRPVPQRVLGE 347

Query: 332 YLAWLMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
           +L   + S    + F+ + +G+ R +L   DVK   + +PP++EQ  I   I  E   +D
Sbjct: 348 FLFRSIGSTRTAQQFHVLATGVTRFALGKHDVKNAIIALPPVEEQQAICRWIVEECQPLD 407

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
             + + E+ I L++E R   IA  VTGQID+RG
Sbjct: 408 EAIARAEEEIQLIREYRDRLIADVVTGQIDVRG 440


>gi|320352395|ref|YP_004193734.1| restriction modification system DNA specificity domain-containing
           protein [Desulfobulbus propionicus DSM 2032]
 gi|320120897|gb|ADW16443.1| restriction modification system DNA specificity domain protein
           [Desulfobulbus propionicus DSM 2032]
          Length = 357

 Score =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 100/301 (33%), Positives = 146/301 (48%), Gaps = 45/301 (14%)

Query: 154 IGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTK---- 209
           I N+ +P+  + EQ  I + +  ET RIDTL+T++ R I LL EK+ AL+S  VT+    
Sbjct: 59  IQNLAVPLGTIPEQTAIADFLDRETGRIDTLVTKKRRLIALLGEKRTALISRTVTRGLPA 118

Query: 210 ------GLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT--------ELNRKNTK-LIES 254
                 GL P  + KDSGIEW+G VP+ WEV  F   V         E    +T  LI  
Sbjct: 119 EAAREFGLKPHTRFKDSGIEWLGEVPEGWEVVKFSREVKIAEGQVDPEREPYSTMVLIGP 178

Query: 255 NILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERG 314
             +    G ++ +    +       Y  ++    GE+++  I     + +LR     +  
Sbjct: 179 EHVEAGTGRLVSEATAEDQAAISGKYYCHK----GEVIYSKI-----RPALRKVVKAKND 229

Query: 315 IITSAYMAVKPHG----IDSTYLAWLMRS--YDLCKVF----YAMGSGLRQSLKFEDVKR 364
            + SA M   P G    + + Y+ WL  S  +    V      AM    R +L   +  R
Sbjct: 230 CLCSADM--YPLGGRDKLLNDYIYWLFLSDQFAAWSVLEADRVAMPKINRNTL---NELR 284

Query: 365 LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           LP  VP   EQ  I   +N ETA+ID L  K+E +IV L E R++ I AAVTG+ID+RG+
Sbjct: 285 LP--VPVGSEQAAIATYLNRETAKIDQLFTKVEAAIVRLLEYRTALITAAVTGKIDVRGK 342

Query: 425 S 425
           +
Sbjct: 343 A 343



 Score = 94.0 bits (232), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/222 (28%), Positives = 106/222 (47%), Gaps = 4/222 (1%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTS---ESGKDIIYIGLEDVESGTG 61
           K + ++KDSG++W+G +P+ W+VV   R  K+  G+     E    ++ IG E VE+GTG
Sbjct: 127 KPHTRFKDSGIEWLGEVPEGWEVVKFSREVKIAEGQVDPEREPYSTMVLIGPEHVEAGTG 186

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
           + + +     Q+  S      KG+++Y K+ P LRK + A  D +CS     L  +D L 
Sbjct: 187 RLVSEATAEDQAAISGKYYCHKGEVIYSKIRPALRKVVKAKNDCLCSADMYPLGGRDKLL 246

Query: 122 ELLQGWLLSIDVTQRIEAI-CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
                WL   D       +  +   M   +   +  + +P+P  +EQ  I   +  ET +
Sbjct: 247 NDYIYWLFLSDQFAAWSVLEADRVAMPKINRNTLNELRLPVPVGSEQAAIATYLNRETAK 306

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
           ID L T+    I  L E + AL++  VT  ++   K    G+
Sbjct: 307 IDQLFTKVEAAIVRLLEYRTALITAAVTGKIDVRGKADKQGL 348



 Score = 43.9 bits (102), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 319 AYMAVKPHGIDSTYLAWLMRSYDL-CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFD 377
           A +   P   D  ++ + ++S +    V  +   G +Q++    ++ L V +  I EQ  
Sbjct: 15  AAIRCNPSRADKRFIYFYLQSKEFQTGVELSWSFGTQQNIGMGVIQNLAVPLGTIPEQTA 74

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           I + ++ ET RID LV K  + I LL E+R++ I+  VT
Sbjct: 75  IADFLDRETGRIDTLVTKKRRLIALLGEKRTALISRTVT 113


>gi|257095818|ref|YP_003169459.1| type I restriction-modification system specificity subunit
           [Candidatus Accumulibacter phosphatis clade IIA str.
           UW-1]
 gi|257048342|gb|ACV37530.1| type I restriction-modification system specificity subunit
           [Candidatus Accumulibacter phosphatis clade IIA str.
           UW-1]
          Length = 475

 Score =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 106/445 (23%), Positives = 197/445 (44%), Gaps = 34/445 (7%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESG----T 60
           K Y +YK+SG+ W+G +P HW V   +    L  G    + +D +  G+  V  G    T
Sbjct: 6   KPYAEYKESGLLWLGQVPGHWDVRKPRHIGSLLKG-VGGTKEDALPAGVPCVRYGELYTT 64

Query: 61  GKYL---PKD--GNSRQSDTSTVSIFAKGQILYGKLGPYLR---KAIIADFDG--ICSTQ 110
             Y    PK      R +D + +     G +L+   G  L    K+ +   DG  +C   
Sbjct: 65  HAYFVRRPKTFIHADRAADYTPLHY---GDVLFAASGETLEDIGKSAVNLIDGTAVCGGD 121

Query: 111 FLVLQPKDVLPELLQGWLLSI-DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
            ++L+P   +     G+++    +  +   +  G T+ H     + ++  P+PP+ EQ  
Sbjct: 122 VIILRPSVPVHAPFLGYVMDCRPLANQKATMGRGTTVKHVYPDELKHLVFPLPPVPEQAA 181

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +     R++  I  + + I LL E+KQA+V   VT+GL+P V +K SGI W+G +P
Sbjct: 182 IVRFLNWANGRLERAIRAKRKVIALLNEQKQAIVHRAVTRGLDPSVPLKPSGIPWLGDIP 241

Query: 230 DHWEV--KPFFAL-VTELNRKNTKLIESNIL-SLSYGNIIQKLETRNMGLKPES-----Y 280
            HW V    F AL + +      +  ++    ++   +I+  +   +   K  S     +
Sbjct: 242 RHWRVWRLKFVALNIVDCLHATPRYSDAGTHPAIRTADIVAGVVLVDQAKKVSSRDYARW 301

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGID--STYLAWLMR 338
            T      G+I++     + ++  + +       +  S  M V        S ++ WL+ 
Sbjct: 302 TTRLQPQEGDILY---SREGERFGIAACVPAATQLCISQRMMVFRIATQHCSKFVMWLLN 358

Query: 339 SYD-LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           S     +    +       +    ++   + +P  +EQ  +   I  ET  I+V +++++
Sbjct: 359 SRSTYGQALQDVMGATAPHVNISTIRNYYLALPLKREQEAVVERIGAETHPIEVAIDRLK 418

Query: 398 QSIVLLKERRSSFIAAAVTGQIDLR 422
           + I LL+E R+  IA  VTG++D+R
Sbjct: 419 REIELLREYRTRLIADVVTGKVDVR 443


>gi|309780966|ref|ZP_07675705.1| type I restriction enzyme, S subunit [Ralstonia sp. 5_7_47FAA]
 gi|330824638|ref|YP_004387941.1| hypothetical protein Alide2_2050 [Alicycliphilus denitrificans
           K601]
 gi|308920269|gb|EFP65927.1| type I restriction enzyme, S subunit [Ralstonia sp. 5_7_47FAA]
 gi|329310010|gb|AEB84425.1| hypothetical protein Alide2_2050 [Alicycliphilus denitrificans
           K601]
          Length = 474

 Score =  109 bits (273), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 109/450 (24%), Positives = 198/450 (44%), Gaps = 49/450 (10%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           YP Y+    +W+  +P+HW ++  K F +    R+    + ++ + ++            
Sbjct: 7   YPNYQPLRSRWVPRVPEHWSLLRAKNFLREIDDRSKAGEETLLSMRMQR----------- 55

Query: 67  DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQG 126
            G    +D S   I  +  I Y K  P   + ++       +  F   QP  V P+    
Sbjct: 56  -GLVPHNDVSVKRIAPENLIGYKKAQP--DELVLNRMQAGNAMFFRNRQPGLVSPDYAVF 112

Query: 127 WLLSIDVTQRIEAICEGATMS---HADWKGIGN---------------IPMPIPPLAEQV 168
            LL  D  + +  +     M     ++ KG+G                + +P+PP  EQ 
Sbjct: 113 RLLRDDNPEYLGHLFRSWPMRGLFRSESKGLGTGTSGFLRLYSDRFTALEIPLPPRPEQD 172

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I   + A+   I   I  +   I+LL E+K  ++ + VT GL+  V +K SGIEW+G V
Sbjct: 173 QIVAYLRAQDAHIARFIQVKRDLIKLLTEQKLRIIDHAVTHGLDASVTLKPSGIEWLGEV 232

Query: 229 PDHWEVKPFFALVTELN----RKNTKLIESNILSLSYGNIIQKLE-TRNMGLKPESYETY 283
           P+HWEV  F   + ++      K++   E+ +   +Y ++ +    T +M L   +    
Sbjct: 233 PEHWEVA-FIKHIADVRFSGVDKHSHDHETPVRLCNYTDVYKNDRITGDMDLMRATATEA 291

Query: 284 QI----VDPGEIVFRFIDLQNDKRSLRSAQVMER--GIITSAYMAV---KPHGIDSTYLA 334
           +I    +  G+++        D   +  A V E   G++ + ++ +    P+ +   +L 
Sbjct: 292 EIARLTLKAGDVILTKDSETPDDIGV-PAWVPEDLPGVVCAYHLGLLRPVPNRVLGEFLF 350

Query: 335 WLMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
             + S    + F+ + +G+ R +L   DVK   V +PP++EQ  I   I  E   +D  +
Sbjct: 351 RAIGSARTAQQFHVLATGVTRFALGKHDVKNAVVALPPVEEQQSICRWITNECQPLDDAI 410

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            + E+ I L++E R   IA  VTGQ+D+RG
Sbjct: 411 ARTEEEIKLIREYRDRLIADVVTGQVDVRG 440


>gi|326387108|ref|ZP_08208718.1| type I restriction-modification methylase S subunit
           [Novosphingobium nitrogenifigens DSM 19370]
 gi|326208289|gb|EGD59096.1| type I restriction-modification methylase S subunit
           [Novosphingobium nitrogenifigens DSM 19370]
          Length = 318

 Score =  109 bits (273), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 89/305 (29%), Positives = 147/305 (48%), Gaps = 28/305 (9%)

Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQAL 202
           GAT    + + + N    +PP AEQ  I   +  E  +ID L  E+ R I LLKEK+QA+
Sbjct: 10  GATFRALNLEPLANTLGCLPPFAEQEAIAGFLDREVGKIDRLAAEQERLIALLKEKRQAV 69

Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESN------- 255
           +S+ VTKGLNP+  +KDSGIEW+  +P HWEV     +V  + +  +   ++        
Sbjct: 70  ISHAVTKGLNPNAPLKDSGIEWLCQIPAHWEVVRIKHVVVTIEQGWSPQCDATPADGPEQ 129

Query: 256 --ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDL----QNDKRSLRSAQ 309
             +L +   N  +   + N  L P+  E        E+  R  DL     N +  + SA 
Sbjct: 130 WGVLKVGCVNGDRFNASENKAL-PDDLEPLP-----ELSLRAGDLLISRANTRELVGSAA 183

Query: 310 VMERG-----IITSAY-MAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSL---KFE 360
           ++E+      +    Y + ++       +L   +RS  +        SG   S+      
Sbjct: 184 LVEQDHDHLLLCDKLYRLRLQTSVASPEFLTLFLRSSMVRGQIEIAASGASSSMLNIGQS 243

Query: 361 DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
            +  + + +PP+ EQ +I   I     +I+ L+   + +I LL+ERR++ I+AAVTG+ID
Sbjct: 244 VILEMALPLPPLGEQGEIATWILKCREQIEALINDAQSAITLLQERRAALISAAVTGKID 303

Query: 421 LRGES 425
           +R  +
Sbjct: 304 VRAAA 308



 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 102/235 (43%), Gaps = 27/235 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFT-------KLNTGRTSESGKD---IIYIGL---EDVE 57
           KDSG++W+  IP HW+VV IK                T   G +   ++ +G    +   
Sbjct: 85  KDSGIEWLCQIPAHWEVVRIKHVVVTIEQGWSPQCDATPADGPEQWGVLKVGCVNGDRFN 144

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGP--YLRKAIIADFDG----ICSTQF 111
           +   K LP D          +S+ A G +L  +      +  A + + D     +C   +
Sbjct: 145 ASENKALPDD----LEPLPELSLRA-GDLLISRANTRELVGSAALVEQDHDHLLLCDKLY 199

Query: 112 -LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHAD--WKGIGNIPMPIPPLAEQV 168
            L LQ     PE L  +L S  V  +IE    GA+ S  +     I  + +P+PPL EQ 
Sbjct: 200 RLRLQTSVASPEFLTLFLRSSMVRGQIEIAASGASSSMLNIGQSVILEMALPLPPLGEQG 259

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
            I   I+    +I+ LI +    I LL+E++ AL+S  VT  ++      ++ +E
Sbjct: 260 EIATWILKCREQIEALINDAQSAITLLQERRAALISAAVTGKIDVRAAAANTTVE 314



 Score = 41.6 bits (96), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
           ++G    ++L  E +      +PP  EQ  I   ++ E  +ID L  + E+ I LLKE+R
Sbjct: 7   SIGGATFRALNLEPLANTLGCLPPFAEQEAIAGFLDREVGKIDRLAAEQERLIALLKEKR 66

Query: 408 SSFIAAAVT 416
            + I+ AVT
Sbjct: 67  QAVISHAVT 75


>gi|329123045|ref|ZP_08251616.1| type I site-specific restriction-modification system, S subunit
           [Haemophilus aegyptius ATCC 11116]
 gi|327471976|gb|EGF17416.1| type I site-specific restriction-modification system, S subunit
           [Haemophilus aegyptius ATCC 11116]
          Length = 408

 Score =  109 bits (273), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 111/426 (26%), Positives = 193/426 (45%), Gaps = 37/426 (8%)

Query: 15  VQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK-DGNSRQS 73
           + W+G +P HW+   +KR  +L   +  +       + L       GK + K D    ++
Sbjct: 1   MDWLGEVPSHWE---LKRLKQLFVEKKHKQS-----LSLNCGAISFGKVIEKSDDKVTEA 52

Query: 74  DTSTVSIFAKGQILYGKLGPY-----LRKAIIADFDGICSTQFLVLQPKDVLPELLQGWL 128
              +     KG+ L   L        LR A+ ++ D + S  ++VL+ K ++ +    +L
Sbjct: 53  TKRSYQEVLKGEFLINPLNLNYDLISLRIAL-SEIDVVVSAGYIVLKEKQIINKKYFSYL 111

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITER 188
           L       ++ +  G   +  ++  I +  + IPPL+EQ  I + +  +T +ID  +   
Sbjct: 112 LHRYDVAYMKLLGSGVRQT-INYGHISDSILVIPPLSEQQKIAQFLDDKTAKIDQAVDLA 170

Query: 189 IRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTEL---- 244
            + I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HWEV     +V E     
Sbjct: 171 EKQIALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWEVVSMKRVVKEHSGNG 230

Query: 245 -------NRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
                  N  N   ++ +  S +    I K    ++  K    + + IV    IV   I 
Sbjct: 231 FPIDLQGNNGNIPFLKVSDFSENQDKYIFKW-NNSVTNKVIKQKKWNIVPKNSIVTAKIG 289

Query: 298 --LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQ 355
             L+ + R + S       II +  + ++    D  +  +L  + D   +F     G   
Sbjct: 290 EALRKNHRKILSID----SIIDNNCLGIEIKKADVLFGYYLHCALDF-DLF--TNPGAIP 342

Query: 356 SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAV 415
           SL  +  +   +++PP +EQ +I + +  +TA+ID  +      I  LKE +S  I   V
Sbjct: 343 SLAMDKYRNQKIVLPPFQEQQEIADYLEQQTAKIDQAIALKTAHIEKLKEYKSVLINDVV 402

Query: 416 TGQIDL 421
           TG++ +
Sbjct: 403 TGKLQV 408



 Score = 74.3 bits (181), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 97/213 (45%), Gaps = 18/213 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGR-----TSESGKDIIYIGLEDVESGTGKYLP 65
           KDSGV+WIG +P+HW+VV +KR  K ++G         +  +I ++ + D      KY+ 
Sbjct: 200 KDSGVEWIGQVPEHWEVVSMKRVVKEHSGNGFPIDLQGNNGNIPFLKVSDFSENQDKYIF 259

Query: 66  KDGNSRQSDT---STVSIFAKGQILYGKLGPYLRKAI--IADFDGICSTQFLVLQPK--D 118
           K  NS  +        +I  K  I+  K+G  LRK    I   D I     L ++ K  D
Sbjct: 260 KWNNSVTNKVIKQKKWNIVPKNSIVTAKIGEALRKNHRKILSIDSIIDNNCLGIEIKKAD 319

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           VL        L  D+     AI   A   + + K      + +PP  EQ  I + +  +T
Sbjct: 320 VLFGYYLHCALDFDLFTNPGAIPSLAMDKYRNQK------IVLPPFQEQQEIADYLEQQT 373

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGL 211
            +ID  I  +   IE LKE K  L++ +VT  L
Sbjct: 374 AKIDQAIALKTAHIEKLKEYKSVLINDVVTGKL 406


>gi|289523861|ref|ZP_06440715.1| type I restriction enzyme, S subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289502517|gb|EFD23681.1| type I restriction enzyme, S subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 489

 Score =  109 bits (272), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 116/453 (25%), Positives = 197/453 (43%), Gaps = 41/453 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           + + K YP YKDSGV W+G +P+HW+V   K   +    R+    ++++      V S  
Sbjct: 2   ITNLKPYPAYKDSGVPWLGHVPEHWEVRRGKTLFRCIDVRSQTGQEELL-----TVSSER 56

Query: 61  GKYLPKDGNSRQSDTSTV---SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
           G    +  N       +     +     ++   L  + R   ++ + GI S+ + V + +
Sbjct: 57  GVVPRRSANVTMFKAESYVGYKLCWPDDLVINSLWAWARGLGVSPYHGIVSSAYGVYRLR 116

Query: 118 DVL---PELLQGWLLSIDVTQRIEAICEGATMSH---ADWKGIGNIPMPIPPLAEQVLIR 171
           +     P  +   + S      +    +G  +S     D   +G    P+PP  EQ  I 
Sbjct: 117 NRQQDNPRFIHQLVRSTPFQWELLVRSKGIWVSRLQLTDDAFLG-ASFPMPPSNEQTAIV 175

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLN-----PDVKMKDSGIEWVG 226
             +     RI   I  + + I+LL+E KQAL+   VT  ++     P    KDSG+EW+G
Sbjct: 176 RFLDYIDRRIWRYIRAKQKLIKLLEEYKQALIHQAVTGQIDVRTGKPYPAYKDSGVEWLG 235

Query: 227 LVPDHWEVKPFFALV---------TELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
            VP+HWE++   + V         +E N K+  L    +       +   L+   M    
Sbjct: 236 EVPEHWEIRRLGSSVRGCVNGVWGSEPNGKD-DLPCVRVADFDRSRLRVHLDKPTMRAIS 294

Query: 278 ESYETYQIVDPGEIVFRFI---DLQNDKRSLRSAQVMERGIITSAYMAVKP--HGIDSTY 332
            S    ++++PG+++       DLQ   R +          +TS ++A  P  +G DS Y
Sbjct: 295 SSDRVRRLLEPGDLLLEKSGGGDLQPVGRVVLYDHPTV--AVTSNFIARMPVENGYDSIY 352

Query: 333 LAWL---MRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           L +L   + S +L        +G+ Q+L         V  PP+ EQ  I   ++ +TA+I
Sbjct: 353 LTYLHAALYSIELNVRSIKQTTGI-QNLDSRTYLSELVAFPPLPEQTAIVEYLDTQTAKI 411

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           D  +      I LL+E R+  IA  VTG++D+R
Sbjct: 412 DAAISAARSEIELLREYRTRLIADVVTGKVDVR 444


>gi|258545847|ref|ZP_05706081.1| type I restriction-modification system specificity determinant
           [Cardiobacterium hominis ATCC 15826]
 gi|258518863|gb|EEV87722.1| type I restriction-modification system specificity determinant
           [Cardiobacterium hominis ATCC 15826]
          Length = 465

 Score =  109 bits (272), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 106/440 (24%), Positives = 189/440 (42%), Gaps = 30/440 (6%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
           +  YP Y+ + ++W   +P+ W ++  K+  +L   +   + +  +      +     K 
Sbjct: 2   FGPYPDYRRTDLKWFEYLPESWGILRAKQMFRLVIEKAPANNQMELLSVYTHIGVRPRKS 61

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-----KD 118
           L + GN + S T    +  +G I+  KL  ++     + + G+ S  + +L+P      D
Sbjct: 62  LEQRGN-KASTTDGYWVVKEGDIICNKLLAWMGAIGASHYQGVTSPAYDILRPVKPCNTD 120

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
               L +          R   I +     + D    G IP+P+P  +EQ  I   + A+ 
Sbjct: 121 YYHFLFRTKKYLQQFKIRSRGIMDMRLRLYFD--QFGQIPIPVPSRSEQDQIVAYLRAQD 178

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
             I   I  +   I+LL E+K  ++ + VT+GL+  V ++ SGIEW+G VP+HWEV+   
Sbjct: 179 AYIARFIKAKRDLIKLLTEQKLRIIDHAVTRGLDSSVALRPSGIEWLGEVPEHWEVQ--- 235

Query: 239 ALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMG-LKPESYETYQI----VDPGEIVF 293
            L    N    K++ +   +   G+    L + N+  +KP+  +  ++     +  ++  
Sbjct: 236 RLKNVANMVLGKMLTTEAKA-GDGDFKPYLRSTNVQWIKPDVRDVKEMWVAKAEMAQLRI 294

Query: 294 RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGL 353
           R  DL   +        M    +   Y+    H + +     +M    L   F+  G   
Sbjct: 295 RKGDLLVSEGGEVGRACMWNDELPECYIQNSVHRVAAKP---MMLPEFLFHQFFTYGKRG 351

Query: 354 R----------QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
           R            L  E +  +P  VPPI+EQ  I   I  E   +D  + + E+ I L+
Sbjct: 352 RFNAIVNRVSIAHLTREKLVTVPFTVPPIEEQKAICRWITEECQPLDDAIARAEEEIKLI 411

Query: 404 KERRSSFIAAAVTGQIDLRG 423
           +E R   IA  VTGQ+D+RG
Sbjct: 412 REYRDRLIADVVTGQVDVRG 431


>gi|288553769|ref|YP_003425704.1| Type 1 restriction-modification system (S) endonuclease subunit
           [Bacillus pseudofirmus OF4]
 gi|288544929|gb|ADC48812.1| Type 1 restriction-modification system (S) endonuclease subunit
           [Bacillus pseudofirmus OF4]
          Length = 443

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 118/430 (27%), Positives = 197/430 (45%), Gaps = 39/430 (9%)

Query: 25  WKVVPIKRFTKL----NTGRTSESGKD-IIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           W+V+ IKR   +        T E  +D + ++  E V++G   +  K G   Q D     
Sbjct: 16  WQVMKIKRVLDIPITDGPHETPELLEDGVPFLSAESVKNGNLNFDLKRGYISQEDHEKYI 75

Query: 80  IFAKGQ---ILYGKLGPYLRKAIIADFD---GICSTQFLVLQPKD-VLPELLQGWLLSID 132
              K Q   I   K G       + D D    I S   L+   K+ V+P+ L  ++ S+ 
Sbjct: 76  KKCKPQRDDIFMVKSGATTGNIAMVDTDEEFSIWSPLALIRAKKEIVIPKYLYYFVGSLA 135

Query: 133 VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFI 192
             +++E      T  +   K I N+ + IP L  Q  I   I  +   ID LI ++ +FI
Sbjct: 136 FREQVEVSWSYGTQQNIGMKVIENLFISIPSLEIQKRIVRYIEYKVKDIDILIKQKGKFI 195

Query: 193 ELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTK-- 250
           +LL++++Q++++  VTKGLNP++ MKDSG++W+G +P+HWEVK        +    T   
Sbjct: 196 KLLEQQRQSILTEAVTKGLNPNMNMKDSGVKWIGEIPEHWEVKKVKHFAIHVGSGKTPSG 255

Query: 251 ----LIESNILSLSYGNI-IQKLETRNMGLKP----ESYETYQIVDPGEIVFRFIDLQND 301
                ++  I  L   N+    +  +++        E  +T Q V P +I+         
Sbjct: 256 GAEIYLDEGIPFLRSLNVHFDGIHLKDLAFISEEINEEMKTSQ-VQPLDILLNITGASIG 314

Query: 302 KRSL------RSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLC--KVFYAMGSGL 353
           + ++      R+       II      V P+     Y   LM S D+   ++++A     
Sbjct: 315 RTTIVPKDFGRANVNQHVCIIRLNQNKVYPY-----YFNMLMAS-DVINQQIWFAQNGSS 368

Query: 354 RQSLKFEDVKRLPVLVPP-IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIA 412
           R+ L F  V+ L   +PP ++EQ +I   I  +  +I  L+  +++ I  LKE R S I 
Sbjct: 369 REGLNFAQVRELIFAIPPTLEEQREINEWIYNKQMKIFNLINLVKEQIEKLKEYRQSLIY 428

Query: 413 AAVTGQIDLR 422
            AVTG+ID+R
Sbjct: 429 EAVTGKIDVR 438



 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 93/216 (43%), Gaps = 22/216 (10%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFT-KLNTGRTSESGKDI-----------IYIGLEDVES 58
           KDSGV+WIG IP+HW+V  +K F   + +G+T   G +I           + +  + +  
Sbjct: 221 KDSGVKWIGEIPEHWEVKKVKHFAIHVGSGKTPSGGAEIYLDEGIPFLRSLNVHFDGIHL 280

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA--DFDGICSTQFLV--- 113
               ++ ++ N  +  TS V       IL    G  + +  I   DF      Q +    
Sbjct: 281 KDLAFISEEINE-EMKTSQVQPL---DILLNITGASIGRTTIVPKDFGRANVNQHVCIIR 336

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP-LAEQVLIRE 172
           L    V P      + S  + Q+I     G++    ++  +  +   IPP L EQ  I E
Sbjct: 337 LNQNKVYPYYFNMLMASDVINQQIWFAQNGSSREGLNFAQVRELIFAIPPTLEEQREINE 396

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            I  + ++I  LI      IE LKE +Q+L+   VT
Sbjct: 397 WIYNKQMKIFNLINLVKEQIEKLKEYRQSLIYEAVT 432


>gi|296330135|ref|ZP_06872617.1| restriction modification system DNA specificity domain protein
           [Bacillus subtilis subsp. spizizenii ATCC 6633]
 gi|305673379|ref|YP_003865051.1| Type I restriction modification system DNA specificity domain
           protein (HsdS) [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296152724|gb|EFG93591.1| restriction modification system DNA specificity domain protein
           [Bacillus subtilis subsp. spizizenii ATCC 6633]
 gi|305411623|gb|ADM36742.1| Type I restriction modification system DNA specificity domain
           protein (HsdS) [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 433

 Score =  107 bits (268), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 113/440 (25%), Positives = 200/440 (45%), Gaps = 48/440 (10%)

Query: 12  DSGVQWIGAIPKHWKVVPIKRF-----TKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           +S +Q +GAIP HW +  +K         +  G    + K  I I  E  +    + L K
Sbjct: 5   ESNIQGVGAIPSHWNIKKLKHCLLPGSEGIKIGPFGSALKSEILI-TEGYKVYGQENLIK 63

Query: 67  D---------GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF--DGICSTQFLVLQ 115
           D            + ++  +  I  +  +L   +G   +  ++      GI  +  + ++
Sbjct: 64  DDFTLGHRFISEEKFNELKSYEII-ENDVLISMMGTVGKCKVVPSIIEKGIMDSHLIRIR 122

Query: 116 PKD--VLPELLQGWLL--SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
             +  +LPE    +L+  SI +  +I+   +G+ MS  +   I N+ + +PP+ EQ +I 
Sbjct: 123 FNESIILPEF-AAYLIQDSIYIKVQIDLNSKGSIMSGLNSSIIKNLKLILPPIEEQRIIL 181

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
           + I  + +++  L   +   I LL E++Q++++  VTKGLNP+VKMK+SGIEW+G +P+H
Sbjct: 182 KYISRKNMQLYQLSNSKNILINLLNEQRQSIITEAVTKGLNPNVKMKNSGIEWIGEIPEH 241

Query: 232 WEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEI 291
           W++K        L+ K   L      S   G + +K+         + Y    ++D  + 
Sbjct: 242 WDMKKVKYTFNNLDYKRIPL-----SSEERGKMTEKVY--------DYYGASGVIDKVDY 288

Query: 292 VF---RFIDLQNDKRSLRSAQV----MERGI--ITSAYMAVKPHGIDSTYLAWLMRSYDL 342
                  I +  D  +L S       + RG   + +    +KP   D  Y   L+ S D 
Sbjct: 289 YLFDETLILIGEDGANLFSRSTPLAFLARGKYWVNNHAHILKPKNGDIDYFVNLLESIDY 348

Query: 343 CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
               Y  GS  +  L  E +  + + +PPI+EQ +I  ++         ++  ++  I  
Sbjct: 349 S--IYISGSA-QPKLTQEALGNITLPLPPIEEQSEIGELVKNVLIEHKEIISTLKNQIEK 405

Query: 403 LKERRSSFIAAAVTGQIDLR 422
           LKE R S I  AVTG+ID+R
Sbjct: 406 LKEYRQSLIYEAVTGKIDVR 425



 Score = 59.7 bits (143), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 90/206 (43%), Gaps = 22/206 (10%)

Query: 11  KDSGVQWIGAIPKHWKVVPIK-RFTKLNTGRTSESGKDIIYIGLEDVESG--TGKYLPKD 67
           K+SG++WIG IP+HW +  +K  F  L+  R          I L   E G  T K     
Sbjct: 228 KNSGIEWIGEIPEHWDMKKVKYTFNNLDYKR----------IPLSSEERGKMTEKVYDYY 277

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYLRK-----AIIADFDGICSTQFLVLQPKDVLPE 122
           G S   D     +F +  IL G+ G  L       A +A      +    +L+PK+   +
Sbjct: 278 GASGVIDKVDYYLFDETLILIGEDGANLFSRSTPLAFLARGKYWVNNHAHILKPKNGDID 337

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
                L SID +  I     G+       + +GNI +P+PP+ EQ  I E +    +   
Sbjct: 338 YFVNLLESIDYSIYIS----GSAQPKLTQEALGNITLPLPPIEEQSEIGELVKNVLIEHK 393

Query: 183 TLITERIRFIELLKEKKQALVSYIVT 208
            +I+     IE LKE +Q+L+   VT
Sbjct: 394 EIISTLKNQIEKLKEYRQSLIYEAVT 419



 Score = 38.1 bits (87), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 97/226 (42%), Gaps = 32/226 (14%)

Query: 215 VKMKDSGIEWVGLVPDHWEVK----------------PF-FALVTELNRKNTKLIESNIL 257
           +K+ +S I+ VG +P HW +K                PF  AL +E+      LI     
Sbjct: 1   MKLNESNIQGVGAIPSHWNIKKLKHCLLPGSEGIKIGPFGSALKSEI------LITEGYK 54

Query: 258 SLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFR--FIDLQNDKRSLRSA-QVMERG 314
                N+I+  +   +G +  S E +  +   EI+     I +       +    ++E+G
Sbjct: 55  VYGQENLIK--DDFTLGHRFISEEKFNELKSYEIIENDVLISMMGTVGKCKVVPSIIEKG 112

Query: 315 IITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVFYAMGS--GLRQSLKFEDVKRLPVLVP 370
           I+ S  + ++ +   I   + A+L++     KV   + S   +   L    +K L +++P
Sbjct: 113 IMDSHLIRIRFNESIILPEFAAYLIQDSIYIKVQIDLNSKGSIMSGLNSSIIKNLKLILP 172

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           PI+EQ  I   I+ +  ++  L       I LL E+R S I  AVT
Sbjct: 173 PIEEQRIILKYISRKNMQLYQLSNSKNILINLLNEQRQSIITEAVT 218


>gi|149280202|ref|ZP_01886325.1| putative type I restriction-modification system, S subunit
           [Pedobacter sp. BAL39]
 gi|149229039|gb|EDM34435.1| putative type I restriction-modification system, S subunit
           [Pedobacter sp. BAL39]
          Length = 394

 Score =  107 bits (268), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 103/414 (24%), Positives = 180/414 (43%), Gaps = 48/414 (11%)

Query: 28  VPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG--- 84
           + +K    + +G T ESG+   + G  D    T   L K GN    D S   I  +G   
Sbjct: 4   ISVKYIFNIFSGSTPESGQAFFWDG--DHNWFTPDDLGKIGNKIYVDESNRKITDEGVEN 61

Query: 85  ---------QILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQ 135
                     I+  K  P    AI       C+    +L+ K+    +   +   +    
Sbjct: 62  ANLKFGVANSIIITKRAPIGNLAITT-LPSSCNQGCFILEQKNSDINVKYYYYYFLIQKD 120

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
           ++  +  G+T    +   + +   P+P L++Q  I + +  E  +ID LI ++ + + +L
Sbjct: 121 KLNNLGRGSTFLELNADEMKSYKAPLPSLSQQNKIVDYLDNEVAKIDALIEKKTQLVTIL 180

Query: 196 KEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESN 255
           +EKK+A+++  VTKGL+P+V MKDSGI+W+G +P HWE+     L    N K+   + + 
Sbjct: 181 EEKKKAVINQTVTKGLDPNVSMKDSGIQWLGYIPKHWEL---VKLKYVSNLKSGDFLPAE 237

Query: 256 ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSL----RSAQVM 311
                  NI ++ + +  G              G     + D  N +  L    R   + 
Sbjct: 238 -------NIKEEGDFKVFG--------------GNGARGYFDNYNHEGDLILIGRQGALC 276

Query: 312 ERGIITSAYMAVKPHGIDSTYLA-----WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLP 366
                 +       H I    +A     WL +  +L  +     +  +  L  + +K L 
Sbjct: 277 GNINFANEKFWATEHAIVCNPIALFDYYWLGKQLELMNLNQYSLAAAQPGLSVDVIKNLF 336

Query: 367 VLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           ++ PPI EQ  I+N +     +  + V+KI  SI LLKE+R++ I+AAV G+++
Sbjct: 337 IVFPPINEQRSISNYLLELDKKNGLAVKKIRDSIDLLKEKRTAVISAAVNGELN 390



 Score = 53.5 bits (127), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 87/203 (42%), Gaps = 16/203 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           KDSG+QW+G IPKHW++V +K  + L +G    + ++I   G   V  G G     D  +
Sbjct: 203 KDSGIQWLGYIPKHWELVKLKYVSNLKSGDFLPA-ENIKEEGDFKVFGGNGARGYFDNYN 261

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLS 130
            + D           IL G+ G        A+     +   +V  P  +      G  L 
Sbjct: 262 HEGDL----------ILIGRQGALCGNINFANEKFWATEHAIVCNPIALFDYYWLGKQLE 311

Query: 131 IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIR 190
           +     +      A         I N+ +  PP+ EQ  I   ++ E  + + L  ++IR
Sbjct: 312 L---MNLNQYSLAAAQPGLSVDVIKNLFIVFPPINEQRSISNYLL-ELDKKNGLAVKKIR 367

Query: 191 -FIELLKEKKQALVSYIVTKGLN 212
             I+LLKEK+ A++S  V   LN
Sbjct: 368 DSIDLLKEKRTAVISAAVNGELN 390


>gi|282849443|ref|ZP_06258828.1| type I restriction modification DNA specificity domain protein
           [Veillonella parvula ATCC 17745]
 gi|282581147|gb|EFB86545.1| type I restriction modification DNA specificity domain protein
           [Veillonella parvula ATCC 17745]
          Length = 427

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 105/442 (23%), Positives = 185/442 (41%), Gaps = 55/442 (12%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGKYLPKD 67
           + KDSGV+W+G IPK W    + +   L + R+++ S KD  Y  L   + G    L   
Sbjct: 3   EMKDSGVRWLGMIPKSWD---LDKIVSLYSERSTKVSDKD--YPALSVTKQGIVPQLESA 57

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGW 127
             +   D     +  K   +            I++++G CS   +VL PK+ +      +
Sbjct: 58  AKTDNGDNR--KLIKKNDFVINSRSDRRGSCGISEYEGSCSLINIVLAPKNNMVNRYYNY 115

Query: 128 LLSIDV-TQRIEAICEGAT--MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
           L   ++          G    +    W  + NI +P P L EQ  I E +  +  +IDT+
Sbjct: 116 LFKTELFADEFYKWGNGIVDDLWSTKWSNMKNIMVPFPSLEEQQAIAEHLDTKCAQIDTI 175

Query: 185 ITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTEL 244
           I +    IE L+E K+A+++Y V KGL+   +  DSGIEW+  +P HW++K         
Sbjct: 176 IAKEQSVIEKLQEYKRAIITYAVVKGLDITAETADSGIEWIDSIPSHWKIK--------- 226

Query: 245 NRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRS 304
                +LI S  +    G   + L+      +   + +   +   ++V+  ++  ND R 
Sbjct: 227 -----RLIFSAYIRARLG--WKGLKADEYTSEGHPFLSAVNIQNDKLVWEDLNFINDDRY 279

Query: 305 LRSAQVMER-----------GIITSAYMAVKPHG----------------IDSTYLAWLM 337
             S ++              GI   A +   P+G                ++S YL +  
Sbjct: 280 DESPEIKLEIGDLLLVKDGAGIGKCAVVDQLPYGTATTNSSLGVITPYPELNSMYLYYFF 339

Query: 338 RSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
            S         + +G+    L   ++K + V++PP  EQ  I   ++ + A +D ++ + 
Sbjct: 340 ESAIFQNYISRIKNGMGVPHLTQGNLKNIMVIIPPYCEQEAIVTYLDEKCANLDSVILRK 399

Query: 397 EQSIVLLKERRSSFIAAAVTGQ 418
           +  I  L E + S I   VTG+
Sbjct: 400 QSRIDKLTEYKKSLIYEVVTGK 421



 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 53/217 (24%), Positives = 114/217 (52%), Gaps = 18/217 (8%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNI--LSLSYGNIIQKLETRNM 273
           +MKDSG+ W+G++P  W++    +L +E   ++TK+ + +   LS++   I+ +LE+   
Sbjct: 3   EMKDSGVRWLGMIPKSWDLDKIVSLYSE---RSTKVSDKDYPALSVTKQGIVPQLES--- 56

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME-RGIITSAYMAVKP-HGIDST 331
             K ++ +  +++   + V   I+ ++D+R   S  + E  G  +   + + P + + + 
Sbjct: 57  AAKTDNGDNRKLIKKNDFV---INSRSDRRG--SCGISEYEGSCSLINIVLAPKNNMVNR 111

Query: 332 YLAWLMRSYDLCKVFYAMGSGLRQSL---KFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
           Y  +L ++      FY  G+G+   L   K+ ++K + V  P ++EQ  I   ++ + A+
Sbjct: 112 YYNYLFKTELFADEFYKWGNGIVDDLWSTKWSNMKNIMVPFPSLEEQQAIAEHLDTKCAQ 171

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGES 425
           ID ++ K +  I  L+E + + I  AV   +D+  E+
Sbjct: 172 IDTIIAKEQSVIEKLQEYKRAIITYAVVKGLDITAET 208


>gi|239995433|ref|ZP_04715957.1| restriction endonuclease S subunits-like protein [Alteromonas
           macleodii ATCC 27126]
          Length = 407

 Score =  106 bits (265), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 80/272 (29%), Positives = 139/272 (51%), Gaps = 35/272 (12%)

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE--- 233
           ET +IDTLI ++ + I+LLKEK+QA++S+ VTKGLNP   MKDSG+EW+G VP+HW    
Sbjct: 130 ETAKIDTLIEKQQQLIKLLKEKRQAVISHAVTKGLNPYAPMKDSGVEWLGEVPEHWSPAT 189

Query: 234 -VKPFFALVTELNRKNTKLIE-----SNILSLSYGNIIQKLETRNMGLKPE-SYETYQI- 285
            +K   +L   L  +  K  E      +++S ++ N        N G+ P  S E Y++ 
Sbjct: 190 PIKYLSSLKGRLGWQGLKADEYKDDGPHVVSSAHFNN----HEINWGMCPRVSEERYELD 245

Query: 286 ----VDPGEIV----------FRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST 331
               ++ G+I+            ++D    K  L S  ++ R ++             + 
Sbjct: 246 SNIQLESGDILLMKDGAAMGKLAYVDDLPGKACLNSHLLLFRPLLRDDIKT-----FHTK 300

Query: 332 YLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
           ++ +LM++          G+G     +  + +    +++P  +EQ  I   ++ + +++ 
Sbjct: 301 FMFYLMQTEHFQGFIRNNGTGATFLGISQQAIGNHRLILPDYEEQLSIAKFLDEQVSKLS 360

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            L  K  Q + LL ERR++ I+AAVTG+ID+R
Sbjct: 361 ALENKKNQMMALLFERRAALISAAVTGKIDVR 392



 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 94/222 (42%), Gaps = 22/222 (9%)

Query: 7   YPQYKDSGVQWIGAIPKHWK-VVPIKRFTKLNTGRTS----------ESGKDIIYIGLED 55
           Y   KDSGV+W+G +P+HW    PIK  + L  GR            + G  ++     +
Sbjct: 167 YAPMKDSGVEWLGEVPEHWSPATPIKYLSSLK-GRLGWQGLKADEYKDDGPHVVSSAHFN 225

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRK-AIIADFDG--ICSTQFL 112
                    P+    R    S + +   G IL  K G  + K A + D  G    ++  L
Sbjct: 226 NHEINWGMCPRVSEERYELDSNIQL-ESGDILLMKDGAAMGKLAYVDDLPGKACLNSHLL 284

Query: 113 VLQP--KDVLPELLQGWLLSIDVTQRIEAICE----GATMSHADWKGIGNIPMPIPPLAE 166
           + +P  +D +      ++  +  T+  +        GAT      + IGN  + +P   E
Sbjct: 285 LFRPLLRDDIKTFHTKFMFYLMQTEHFQGFIRNNGTGATFLGISQQAIGNHRLILPDYEE 344

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           Q+ I + +  +  ++  L  ++ + + LL E++ AL+S  VT
Sbjct: 345 QLSIAKFLDEQVSKLSALENKKNQMMALLFERRAALISAAVT 386



 Score = 43.9 bits (102), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 43/68 (63%), Gaps = 5/68 (7%)

Query: 352 GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINV---ETARIDVLVEKIEQSIVLLKERRS 408
           G + +L  + V  + V +P  K++ +I  +I+    ETA+ID L+EK +Q I LLKE+R 
Sbjct: 96  GTQLNLNTDTVGSIKVALP--KDEIEIQGIIDFLDHETAKIDTLIEKQQQLIKLLKEKRQ 153

Query: 409 SFIAAAVT 416
           + I+ AVT
Sbjct: 154 AVISHAVT 161


>gi|298529187|ref|ZP_07016590.1| putative type I restriction enzyme, S subunit [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298510623|gb|EFI34526.1| putative type I restriction enzyme, S subunit [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 460

 Score =  106 bits (265), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 73/202 (36%), Positives = 104/202 (51%), Gaps = 7/202 (3%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGK-YLPKDGN 69
           K SGV W+G IPKHW+   +K   +    +TS    D +Y+ LE VE  TG+  LP +  
Sbjct: 222 KPSGVDWLGNIPKHWEKNRLKFLVRNVNEQTSTRQPDEVYVALEHVEGWTGRITLPSED- 280

Query: 70  SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGW 127
                 S V  F  G +L+GKL PYL K       G+C  +FLVL+ K+  +LPE L+  
Sbjct: 281 --IEFGSQVKRFHVGDVLFGKLRPYLAKVTRPSVKGVCVGEFLVLRRKNEALLPEFLEQE 338

Query: 128 LLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL-AEQVLIREKIIAETVRIDTLIT 186
           L S      I +   GA M  ADW  IGN+ +  PP  AEQ+ I      +T  +   I 
Sbjct: 339 LRSKLFIDIINSATFGAKMPRADWDFIGNLLIVYPPTHAEQLEILSDTGKQTASLQAAID 398

Query: 187 ERIRFIELLKEKKQALVSYIVT 208
           +  R + L++E +  L++ +VT
Sbjct: 399 KANREVSLIQEYRTRLIADVVT 420



 Score = 97.4 bits (241), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 104/445 (23%), Positives = 191/445 (42%), Gaps = 49/445 (11%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K Y +YKDSG+ W   IP HWKV   K   +    R+    ++ + +  E          
Sbjct: 6   KPYAEYKDSGLPWASKIPTHWKVRRAKNLFRCIDVRSKTGTEERLTVSAER--------- 56

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGP----------YLRKAIIADFDGICSTQFLV- 113
              G   +S        AK  I + +  P          + R   +A   G+ S+ + V 
Sbjct: 57  ---GVVPRSSMKVTMFEAKSYIGHKRCWPDDLVINSLWAWGRGLGVARHHGLVSSAYGVY 113

Query: 114 -LQPK-DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPI--PPLAEQVL 169
            L+P+ D     +   + S      +    +G  +S         +  PI  P + E   
Sbjct: 114 RLRPEFDEYAPFIHHLVRSKVYHWELRTRSKGVWISRLQLTDDAFLRAPILVPSVEEGKA 173

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   I     +++  I  R R I++L E+KQA+++  VT+GL+P+V +K SG++W+G +P
Sbjct: 174 ITRFIRDIDRKVNAFIRNRRRLIKVLNEQKQAIINRAVTRGLDPNVPLKPSGVDWLGNIP 233

Query: 230 DHWEVKPFFALVTELNRK-NTKLIESNILSLSY-----GNIIQKLETRNMGLKPESYETY 283
            HWE      LV  +N + +T+  +   ++L +     G I    E    G + + +   
Sbjct: 234 KHWEKNRLKFLVRNVNEQTSTRQPDEVYVALEHVEGWTGRITLPSEDIEFGSQVKRFHV- 292

Query: 284 QIVDPGEIVF---RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY 340
                G+++F   R    +  + S++   V E  ++     A+ P      +L   +RS 
Sbjct: 293 -----GDVLFGKLRPYLAKVTRPSVKGVCVGEFLVLRRKNEALLPE-----FLEQELRSK 342

Query: 341 DLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIK-EQFDITNVINVETARIDVLVEKIEQ 398
               +  +   G +     ++ +  L ++ PP   EQ +I +    +TA +   ++K  +
Sbjct: 343 LFIDIINSATFGAKMPRADWDFIGNLLIVYPPTHAEQLEILSDTGKQTASLQAAIDKANR 402

Query: 399 SIVLLKERRSSFIAAAVTGQIDLRG 423
            + L++E R+  IA  VTG++D+R 
Sbjct: 403 EVSLIQEYRTRLIADVVTGKVDVRN 427



 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 49/216 (22%), Positives = 96/216 (44%), Gaps = 10/216 (4%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L P  + KDSG+ W   +P HW+V+    L   ++ ++    E  +   +   ++ +   
Sbjct: 5   LKPYAEYKDSGLPWASKIPTHWKVRRAKNLFRCIDVRSKTGTEERLTVSAERGVVPRSSM 64

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY--MAVKPHGI 328
           +    + +SY  ++   P ++V     L    R L  A+    G+++SAY    ++P   
Sbjct: 65  KVTMFEAKSYIGHKRCWPDDLVIN--SLWAWGRGLGVAR--HHGLVSSAYGVYRLRPEFD 120

Query: 329 D-STYLAWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINV 384
           + + ++  L+RS            G+   R  L  +   R P+LVP ++E   IT  I  
Sbjct: 121 EYAPFIHHLVRSKVYHWELRTRSKGVWISRLQLTDDAFLRAPILVPSVEEGKAITRFIRD 180

Query: 385 ETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
              +++  +    + I +L E++ + I  AVT  +D
Sbjct: 181 IDRKVNAFIRNRRRLIKVLNEQKQAIINRAVTRGLD 216


>gi|148825619|ref|YP_001290372.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae PittEE]
 gi|229845500|ref|ZP_04465629.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 6P18H1]
 gi|148715779|gb|ABQ97989.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae PittEE]
 gi|229811603|gb|EEP47303.1| putative type I site-specific restriction-modification system, S
           subunit [Haemophilus influenzae 6P18H1]
          Length = 358

 Score =  106 bits (265), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 91/343 (26%), Positives = 159/343 (46%), Gaps = 33/343 (9%)

Query: 100 IADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPM 159
           +++ D + S  ++VL+ K ++ +    +LL       ++ +  G   +  ++  I +  +
Sbjct: 24  LSEIDVVVSAGYIVLKEKQIINKKYFSYLLHRYDVAYMKLLGSGVRQT-INYGHISDSIL 82

Query: 160 PIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKD 219
            IPPL+EQ  I + +  +T +ID  +    + I LLKE KQ L+   VT+GLNPDV +KD
Sbjct: 83  VIPPLSEQQKIAQFLDDKTAKIDRAVDLAEKQIALLKEHKQILIQNAVTRGLNPDVPLKD 142

Query: 220 SGIEWVGLVPDHWEVKPF---FALVTELNRKNTKLIESNILSLSYGNIIQKL------ET 270
           SG+EW+G VP+HW++K F   F     L+     L +  I  ++YG +  +       E 
Sbjct: 143 SGVEWIGQVPEHWDIKRFRNLFDFGKGLSITKENLQDEGIPCVNYGEVHSRYGFEVIPER 202

Query: 271 RNMGLKPESYETYQ--IVDPGEIVF-----------RFIDLQNDKRSLRSAQ-VMERGII 316
             +      Y  +   +++ G+ VF            F  L +  R       V+ R  I
Sbjct: 203 DALKCVDSKYLVFNNSMLNKGDFVFADTSEDIEGSGNFTYLNSSTRIFAGYHTVITRLKI 262

Query: 317 TSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQF 376
           T+ +  +  +    ++   +       KVF    S L+ +          VL+P +KEQ 
Sbjct: 263 TAIHRYIAYYFDSLSFRNQIRNKVKGVKVFSITQSILKGTF---------VLLPNLKEQQ 313

Query: 377 DITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
            I + ++ +TA+ID  +      I  LKE +S  I   VTG++
Sbjct: 314 QIADYLDTQTAKIDQAIALKTAHIEKLKEYKSVLINDVVTGKV 356



 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 72/129 (55%), Gaps = 2/129 (1%)

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI-DSTYLAWLMRSYDLCKVFY 347
           GE +   ++L  D  SLR A      ++++ Y+ +K   I +  Y ++L+  YD+  +  
Sbjct: 4   GEFLINPLNLNYDLISLRIALSEIDVVVSAGYIVLKEKQIINKKYFSYLLHRYDVAYM-K 62

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
            +GSG+RQ++ +  +    +++PP+ EQ  I   ++ +TA+ID  V+  E+ I LLKE +
Sbjct: 63  LLGSGVRQTINYGHISDSILVIPPLSEQQKIAQFLDDKTAKIDRAVDLAEKQIALLKEHK 122

Query: 408 SSFIAAAVT 416
              I  AVT
Sbjct: 123 QILIQNAVT 131



 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 96/218 (44%), Gaps = 25/218 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKL-NTGR----TSESGKD--IIYIGLEDVESGTG-K 62
           KDSGV+WIG +P+HW    IKRF  L + G+    T E+ +D  I  +   +V S  G +
Sbjct: 141 KDSGVEWIGQVPEHW---DIKRFRNLFDFGKGLSITKENLQDEGIPCVNYGEVHSRYGFE 197

Query: 63  YLPKDGNSRQSDTSTV----SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
            +P+    +  D+  +    S+  KG  ++      +  +   +F  + S+  +      
Sbjct: 198 VIPERDALKCVDSKYLVFNNSMLNKGDFVFADTSEDIEGS--GNFTYLNSSTRIFAGYHT 255

Query: 119 VLPEL--------LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           V+  L        +  +  S+    +I    +G  +       +    + +P L EQ  I
Sbjct: 256 VITRLKITAIHRYIAYYFDSLSFRNQIRNKVKGVKVFSITQSILKGTFVLLPNLKEQQQI 315

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            + +  +T +ID  I  +   IE LKE K  L++ +VT
Sbjct: 316 ADYLDTQTAKIDQAIALKTAHIEKLKEYKSVLINDVVT 353


>gi|148926926|ref|ZP_01810603.1| putative type I restriction enzyme specificity S protein
           [Campylobacter jejuni subsp. jejuni CG8486]
 gi|145845010|gb|EDK22107.1| putative type I restriction enzyme specificity S protein
           [Campylobacter jejuni subsp. jejuni CG8486]
          Length = 375

 Score =  106 bits (264), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK-----DIIYIGLEDVESGTGKY 63
            +K+SG++W+G IP+HW+VV I +      G   E+       +I  I + D++     Y
Sbjct: 3   NFKESGIEWLGEIPEHWEVVKINKIVTFVNGYAFENFDFNPIFEIPVIRIGDMQKEKILY 62

Query: 64  LPKDGNSRQSDTSTVSIF--AKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
              D   +  +   +  F  +   IL    G    K    D D        V   +  L 
Sbjct: 63  ---DNCLKTKEKEKLKQFLISNNDILIALSGATTGKIAFCDTDNKAYINQRVAIVRSKL- 118

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           +L++ + L+   +  IE  C G+   +   K IG   +P+PPL EQ  I   +  +  +I
Sbjct: 119 KLVKYYFLTRGFSLLIELACNGSAQPNISTKEIGEFKIPLPPLKEQEQIANFLDEKCKKI 178

Query: 182 DTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
              I ++ + I LLKE+KQAL++  +TKGL+ ++  KDSGIEW+G +P HW +
Sbjct: 179 ANFIEKKEKLITLLKEQKQALINETITKGLDKNINFKDSGIEWLGEIPQHWRI 231



 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 99/215 (46%), Gaps = 20/215 (9%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESN----ILSLSYGNI-IQKLETR 271
            K+SGIEW+G +P+HWEV     +VT +N    +  + N    I  +  G++  +K+   
Sbjct: 4   FKESGIEWLGEIPEHWEVVKINKIVTFVNGYAFENFDFNPIFEIPVIRIGDMQKEKILYD 63

Query: 272 NMGLKPESYETYQ-IVDPGEIVFRFIDLQNDKRSL----RSAQVMER-GIITSAYMAVKP 325
           N     E  +  Q ++   +I+         K +       A + +R  I+ S    VK 
Sbjct: 64  NCLKTKEKEKLKQFLISNNDILIALSGATTGKIAFCDTDNKAYINQRVAIVRSKLKLVKY 123

Query: 326 HGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
           +        +L R + L       GS  + ++  +++    + +PP+KEQ  I N ++ +
Sbjct: 124 Y--------FLTRGFSLLIELACNGSA-QPNISTKEIGEFKIPLPPLKEQEQIANFLDEK 174

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
             +I   +EK E+ I LLKE++ + I   +T  +D
Sbjct: 175 CKKIANFIEKKEKLITLLKEQKQALINETITKGLD 209



 Score = 42.0 bits (97), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTG 39
            +KDSG++W+G IP+HW++V +K     N G
Sbjct: 213 NFKDSGIEWLGEIPQHWRIVKLKYVAFTNIG 243


>gi|330506918|ref|YP_004383346.1| type I restriction-modification enzyme, S subunit [Methanosaeta
           concilii GP-6]
 gi|328927726|gb|AEB67528.1| type I restriction-modification enzyme, S subunit [Methanosaeta
           concilii GP-6]
          Length = 418

 Score =  106 bits (264), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 98/391 (25%), Positives = 178/391 (45%), Gaps = 40/391 (10%)

Query: 22  PKHWKVVPIKRFTKLNTGRTSESG-KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           P  WK++ +    +L       +   D+ Y+GLE ++S +   L + G+S + ++S  S 
Sbjct: 7   PSSWKMISLDEVCELRKEAIHPNKYPDLPYVGLEHIDS-SNSILKRSGSSFEVNSSK-SK 64

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEA 139
           F  G ILYGKL PYL K+++ DFDG+CST  LVL+ K+ ++P+ L   + +         
Sbjct: 65  FHSGDILYGKLRPYLDKSVLVDFDGMCSTDILVLKTKESIVPQFLVNIIHTSQFINYAVN 124

Query: 140 ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR-IDTLITERIRFIELLKEK 198
             +G       W  I      +PPL EQ     + IA  +R +      R+R I L +E+
Sbjct: 125 SSKGLNHPRTSWSSISAFKFLLPPLPEQ-----RAIARAMRAVQAAREARLREIALERER 179

Query: 199 KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILS 258
           K AL+ ++ T G     + + + +  +G +P+ W        + +L     K+++    +
Sbjct: 180 KAALMEHLFTHG----TRGEPTKMTEIGEMPESWS-------MIQLEEACIKIVDCPHST 228

Query: 259 LSYGN----IIQKLETRN--MGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME 312
             +      +++    RN  + LK  SY T +  +  E V R    + D    R A V E
Sbjct: 229 PHFSPAGVLVVRNFNIRNGRLDLKFPSYTTEE--EYSERVKRCEPTEGDVLFSREAPVGE 286

Query: 313 RGIITS----------AYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFED 361
             ++              + V    ++  +L  +  S  +  +  A+ SG+  + L   D
Sbjct: 287 ACLVPPDVRLCLGQRMMLLRVDTSKLNRFFLVQVFYSNAIRSIMMAISSGVTAKHLNVAD 346

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           VKRL +    ++EQ  I+++++   ++I  L
Sbjct: 347 VKRLRIPFSSMEEQKQISDILSACDSKITAL 377


>gi|295402727|ref|ZP_06812668.1| restriction modification system DNA specificity domain protein
           [Geobacillus thermoglucosidasius C56-YS93]
 gi|294975226|gb|EFG50863.1| restriction modification system DNA specificity domain protein
           [Geobacillus thermoglucosidasius C56-YS93]
          Length = 472

 Score =  105 bits (263), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 113/419 (26%), Positives = 181/419 (43%), Gaps = 62/419 (14%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           SE  K ++Y+G+EDVE+ TG     +  S     S    F    ILYGKL PYL K  + 
Sbjct: 47  SEEAKRLLYLGMEDVEANTGII---NKISEDVGKSNTYKFDSTHILYGKLRPYLNKVALP 103

Query: 102 DFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
           DF+G C+T+F+ L+P+  +  E L  +L +  V   + A  +G+ M  AD K + +I  P
Sbjct: 104 DFEGRCTTEFIPLKPEGGISREYLALFLRTQKVIDTVMAKSKGSRMPRADMKVLMSIEFP 163

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK-----KQALVSYIVTKGLNP-- 213
           +PP++EQ  I +K+ +    ID +  E  +  ELLK++     ++A    +V +  N   
Sbjct: 164 LPPVSEQRRIIKKVKSYFKIIDKIEKELAKAKELLKKRHESLLQKAFRGELVKREENDKS 223

Query: 214 -----DVKMKDSGIE---------WVGL-----------------VPDHWEVKPFFALVT 242
                ++K+  S  E         WV L                 VP  W     +    
Sbjct: 224 TFDLLNIKVSSSTDENDPYDIPENWVWLELGDCGVITGGGTPSKKVPSFWNGNILWVSPK 283

Query: 243 ELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDK 302
           ++ R      E  I  L+      KL  +N  L                V R   L++  
Sbjct: 284 DMKRDKINDTEDKITELAIEKSSAKLIPKNSVL---------------FVVRSGILRH-- 326

Query: 303 RSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFE 360
            SL  A       +     A+ PH  I+ +YL +  + ++   +  A   G   +SL  E
Sbjct: 327 -SLPVAINDVELTVNQDIKAITPHEFINVSYLFYAFKCFEKSWLQEASKIGATVESLDME 385

Query: 361 DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
            VK+L V VPP+ EQ  I   +  E  +   +V+ IE++   L++ R S +  A  G++
Sbjct: 386 KVKKLKVPVPPLSEQLKIIERLEKEFEKEQAIVQSIERAEEKLQKMRQSLLQKAFRGEL 444



 Score = 40.8 bits (94), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 56/116 (48%), Gaps = 6/116 (5%)

Query: 314 GIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVL---V 369
           G  T+ ++ +KP G I   YLA  +R+  +     A   G R  +   D+K L  +   +
Sbjct: 107 GRCTTEFIPLKPEGGISREYLALFLRTQKVIDTVMAKSKGSR--MPRADMKVLMSIEFPL 164

Query: 370 PPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGES 425
           PP+ EQ  I   +      ID + +++ ++  LLK+R  S +  A  G++  R E+
Sbjct: 165 PPVSEQRRIIKKVKSYFKIIDKIEKELAKAKELLKKRHESLLQKAFRGELVKREEN 220


>gi|126434812|ref|YP_001070503.1| restriction modification system DNA specificity subunit
           [Mycobacterium sp. JLS]
 gi|126234612|gb|ABN98012.1| restriction modification system DNA specificity domain
           [Mycobacterium sp. JLS]
          Length = 451

 Score =  105 bits (263), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 106/453 (23%), Positives = 193/453 (42%), Gaps = 40/453 (8%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD----IIYIGLEDVE-- 57
           + +YP+Y DSGV+W+G +P  W V P+K    +      +   D    +      DV   
Sbjct: 3   WPSYPRYNDSGVEWLGRVPSGWAVSPLKNVATVFPSSVDKHSHDNEIPVQLCNYTDVYKN 62

Query: 58  ---SGTGKYLPKDGNSRQSDTSTV----SIFAKGQILYGKLG--PYLRKAIIADFDGICS 108
              SG   ++       +    T+    +I  K       +G   Y+ + +    D +C 
Sbjct: 63  ERISGALDFMKATATPEEIKKFTLKQGDTIITKDSETADDIGISAYVEETLP---DVLCG 119

Query: 109 TQFLVLQPKDVLPEL----LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
               V++P   LP L    ++    S  +   +E    G T        I N+ +P+PP 
Sbjct: 120 YHLSVVRP---LPGLDGRFVKRLFDSHYLKASMEVSANGLTRVGLGQYAIDNLNIPLPPP 176

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
            EQ+ I + + AET +ID LI ++   I  L+E + A +++ VTKGL+P V M       
Sbjct: 177 DEQLQIADFLEAETAKIDALIAKQEHLIATLREDRTATITHAVTKGLDPTVDMVQPHNSE 236

Query: 225 VGLVPDHWEVKPFFALVTELNR-----KNTKLIES-NILSLSYGNI----IQKLETRNMG 274
           +   P HW +      + E+       K+    E+ ++  L   N+    +   E + + 
Sbjct: 237 LPACPKHWTLLISLKRLAEVQTGLTLGKSVDPAEAVDVPYLRVANVQTSGVNLDEVKTVA 296

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK-PHGIDSTYL 333
           +     + Y + D   ++    D+    R    +  +   I  +   AV+    +   +L
Sbjct: 297 VHRSELKRYLLRDGDVLMTEGGDIDKLGRGCVWSGEIAPCIHQNHVFAVRCSDALSGDFL 356

Query: 334 AWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVL---VPPIKEQFDITNVINVETARID 390
            +L+ +  + + ++ M +    +L   +   L      +PP  EQ +I + +N   A +D
Sbjct: 357 VYLLDTA-VARNYFFMTAKKTTNLASTNSTTLGAFTFSLPPRAEQDEIVDHLNERCAGLD 415

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            L+ K    I +L+E R++ I  AVTG+ID+RG
Sbjct: 416 ALIAKANAVITVLREYRAALITDAVTGKIDVRG 448


>gi|148360829|ref|YP_001252036.1| hypothetical protein LPC_2789 [Legionella pneumophila str. Corby]
 gi|148282602|gb|ABQ56690.1| hypothetical protein LPC_2789 [Legionella pneumophila str. Corby]
          Length = 424

 Score =  105 bits (261), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/192 (33%), Positives = 104/192 (54%), Gaps = 3/192 (1%)

Query: 231 HWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
            W+  P       + + N  LIE + L+L+ G +I +      GL+   Y TYQI +  +
Sbjct: 15  RWKSVPTKRNFRNIKQINKGLIEEHRLALTLGGVIDRSLDDVEGLQSSDYSTYQIFEKDD 74

Query: 291 IVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVFYA 348
           +VF+ IDL+N K S R   V  RGI++ AY+ + P    +   Y  WL  +  +  +F  
Sbjct: 75  LVFKLIDLENIKTS-RVGYVPRRGIMSPAYIRLTPTSELVIPRYYYWLFYAAYINNIFNG 133

Query: 349 MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRS 408
           MG G+RQ+L   D+   P+ + P + Q +ITN ++ E  RID L+EK ++ I L++ER S
Sbjct: 134 MGGGVRQNLTPTDLLEFPIPLTPKETQIEITNFLDREIDRIDQLIEKKKKLICLMRERES 193

Query: 409 SFIAAAVTGQID 420
           + +  A+   I+
Sbjct: 194 NAVREAIFSLIN 205



 Score = 45.1 bits (105), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 95/441 (21%), Positives = 168/441 (38%), Gaps = 92/441 (20%)

Query: 24  HWKVVPIKR----FTKLNTG-----RTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSD 74
            WK VP KR      ++N G     R + +   +I   L+DVE             + SD
Sbjct: 15  RWKSVPTKRNFRNIKQINKGLIEEHRLALTLGGVIDRSLDDVEG-----------LQSSD 63

Query: 75  TSTVSIFAKGQILY----------GKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPE 122
            ST  IF K  +++           ++G   R+       GI S  ++ L P    V+P 
Sbjct: 64  YSTYQIFEKDDLVFKLIDLENIKTSRVGYVPRR-------GIMSPAYIRLTPTSELVIPR 116

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
               WL        I     G    +     +   P+P+ P   Q+ I   +  E  RID
Sbjct: 117 YYY-WLFYAAYINNIFNGMGGGVRQNLTPTDLLEFPIPLTPKETQIEITNFLDREIDRID 175

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKM-KDSGIEWVGL---------VPDHW 232
            LI ++ + I L++E++   V   +   +N  V++ K S +  V            P+ +
Sbjct: 176 QLIEKKKKLICLMRERESNAVREAIFSLINEGVQIWKLSHVCRVQRGKFTHRPRNAPELY 235

Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSY----------GNIIQKLETRNMGLKPESYET 282
           + +  F    ++ R N K I  +  +LS            N +      N+G    +  T
Sbjct: 236 DGEVPFIQTGDVARAN-KFITKHKQTLSELGISVSAKFPSNTLLMAIAANVG--NLAITT 292

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDL 342
           Y++  P  IV                     G I +         ++S YL +++R+   
Sbjct: 293 YEVYCPDSIV---------------------GFIPT-------EKVESEYLYYVLRAISD 324

Query: 343 CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
                +  +  + +     +  L + +P I++Q ++ +   +E   +     KI  SI  
Sbjct: 325 DISSSSTSNA-QDNTNVARLGSLKIPLPSIQKQKNLIDKFKIEENLLFKTTSKISNSITK 383

Query: 403 LKERRSSFIAAAVTGQIDLRG 423
           L E R + I+ AVTGQ+D++ 
Sbjct: 384 LNEFRCALISEAVTGQLDIKS 404


>gi|304315081|ref|YP_003850228.1| type I restriction-modification enzyme, subunit S
           [Methanothermobacter marburgensis str. Marburg]
 gi|302588540|gb|ADL58915.1| predicted type I restriction-modification enzyme, subunit S
           [Methanothermobacter marburgensis str. Marburg]
          Length = 368

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 95/348 (27%), Positives = 164/348 (47%), Gaps = 29/348 (8%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           ++GLE + SG  K    +  S +   ST   F  G ILYGKL PYL KA++AD +GICST
Sbjct: 22  FVGLEHIRSGETKLC--EYVSDEGIRSTKYRFYTGDILYGKLRPYLDKAVLADINGICST 79

Query: 110 QFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
             +VL P D ++PE L  ++ +    QR  +   G       WK I    M +PPL EQ 
Sbjct: 80  DLIVLTPSDRIIPEFLIYFIHTNQFIQRAVSTTSGTNHPRTSWKAISKFRMALPPLEEQ- 138

Query: 169 LIREKIIAETVR-IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
               K I+E ++ +D  I +  + I + ++ K+ L+  ++ +G+N   + KDS    VG 
Sbjct: 139 ----KRISEILQDVDGAIEKVNKEIGVTEKLKRGLMQRLLMEGIN-HTEFKDSP---VGR 190

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
           +P  W+V     L T  N K   ++    + +   N    L +  +  K ++    ++  
Sbjct: 191 IPVDWDVVKLGDLFTFKNGKRPPVLNEGEIPIYGANGKMGLTSNYLKTKDKALIFGRVGS 250

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFY 347
            GE+            S     V +  I T +Y + +   ++  ++ +L++  DL K F 
Sbjct: 251 SGEVHL----------SKGCVWVSDNAIYTESYDSKR---VNVHFMFYLIKFKDL-KRFA 296

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
              +    +  F  +    V +PP++EQ  I+ ++     R+++L E+
Sbjct: 297 TKTTHPIITQTF--INNFKVPLPPLEEQKRISEILQDVDRRLELLTER 342


>gi|264677663|ref|YP_003277569.1| hypothetical protein CtCNB1_1527 [Comamonas testosteroni CNB-2]
 gi|262208175|gb|ACY32273.1| hypothetical protein CtCNB1_1527 [Comamonas testosteroni CNB-2]
          Length = 429

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 105/435 (24%), Positives = 178/435 (40%), Gaps = 33/435 (7%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y  YK S   W+G +P HW V P++  T L   ++ ++  D+  + +   E G      +
Sbjct: 4   YESYKPSEATWLGNVPSHWDVQPLRAVTSL---KSDKNRPDLPVLSVYR-EYGVILKDSR 59

Query: 67  DGNSRQS--DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPE 122
           D N   +  DTST  +   G ++  K+  +     ++   GI S  ++    K     P 
Sbjct: 60  DDNHNATSLDTSTYKVVKPGDLVVNKMKAWQGSMGVSSHHGIVSPAYITCTTKADRARPA 119

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHAD--WKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            L   L S  +     ++  G  +   D  ++    IP+P+PP  EQ  I   +  +T  
Sbjct: 120 YLHYLLRSSPLIGVYNSLSYGVRVGQWDMHYEDFKQIPIPLPPNDEQDRIVAFLDQKTAE 179

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE---VKPF 237
           ID  I ++ R   LLKE++  L++  VTKGL+P+  M      W+   P HW+   +K  
Sbjct: 180 IDAAIEKKERLASLLKEQQFKLINLAVTKGLDPNAAMTCGRSPWIESYPAHWQLMRIKHV 239

Query: 238 FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
              + +   K   + E     +   + ++  E      K     TY+         R I 
Sbjct: 240 LRAIVDTEHKTPPMYEEGPALMVRTSNVKNGELVFKNAKYTDELTYR-----RWTRRAIP 294

Query: 298 LQNDKRSLRSAQVMERGIITSAYMA----------VKPHGIDSTYLAWLMRSYDLCKVF- 346
           +  D    R A   E  ++     A          V P  +D  +    + S    K F 
Sbjct: 295 VAGDILFTREAPAGEACVLPDGIKAAIGQRMVLFKVDPERLDPHFAVHSIYS-GAAKAFI 353

Query: 347 --YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
              ++GS +       D+  +P+L+PP++EQ  I   I     +   L++     I  L+
Sbjct: 354 ELLSVGSTVAH-FNMSDIGNIPLLLPPLQEQQKIAVGIKSIQRQFQPLIDSAANGIEQLQ 412

Query: 405 ERRSSFIAAAVTGQI 419
           E + + IA+AV GQI
Sbjct: 413 ELKRTLIASAVLGQI 427



 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 102/208 (49%), Gaps = 9/208 (4%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           K S   W+G VP HW+V+P  A+ +  + KN   +    +   YG I++     N     
Sbjct: 8   KPSEATWLGNVPSHWDVQPLRAVTSLKSDKNRPDLPVLSVYREYGVILKDSRDDNHNATS 67

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV--KPHGIDSTYLAW 335
               TY++V PG++V   +        + S      GI++ AY+    K       YL +
Sbjct: 68  LDTSTYKVVKPGDLVVNKMKAWQGSMGVSS----HHGIVSPAYITCTTKADRARPAYLHY 123

Query: 336 LMRSYDLCKVFYAMGSGLR---QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           L+RS  L  V+ ++  G+R     + +ED K++P+ +PP  EQ  I   ++ +TA ID  
Sbjct: 124 LLRSSPLIGVYNSLSYGVRVGQWDMHYEDFKQIPIPLPPNDEQDRIVAFLDQKTAEIDAA 183

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQID 420
           +EK E+   LLKE++   I  AVT  +D
Sbjct: 184 IEKKERLASLLKEQQFKLINLAVTKGLD 211


>gi|114320942|ref|YP_742625.1| restriction modification system DNA specificity subunit
           [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227336|gb|ABI57135.1| restriction modification system DNA specificity domain protein
           [Alkalilimnicola ehrlichii MLHE-1]
          Length = 419

 Score =  103 bits (258), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 101/357 (28%), Positives = 160/357 (44%), Gaps = 34/357 (9%)

Query: 84  GQILYGKLGPYLR---KAIIADFDGICSTQFLVLQP-KDVLPELLQGWLL-SIDVTQRIE 138
           G IL   +  YLR   K   A  D I ST F V++P ++ +     GW   S      + 
Sbjct: 72  GDILISTVRTYLRAIAKVDEASPDLIASTGFCVVRPDREEVDSGYLGWAAKSEPFVSEVV 131

Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK 198
           +   G +    +   +  I MP+PPL  Q  I + +  +T RID LI ++   ++ L EK
Sbjct: 132 SRSVGVSYPAINASELVTIEMPLPPLETQRRIAQFLDEKTARIDGLIEKKRALLDRLAEK 191

Query: 199 KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT---------ELNRKNT 249
           +QAL++  VTKGLNP+  MK SGI+W+G +P HW++ PF              E    + 
Sbjct: 192 RQALITRAVTKGLNPEAPMKPSGIDWLGDIPAHWDLVPFKWRCQVQSGQVDPREPEYTDM 251

Query: 250 KLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQ 309
            LI  + +    G +         G     Y        G +++  I     + +LR   
Sbjct: 252 PLIAPDYIESGTGRLYDVPSAEEQGAISGKY----FCSEGSVLYSKI-----RPALRKVA 302

Query: 310 VMERGIITSAYM-AVKPHG-IDSTYLAWLMRSYDLCKVF--YAMGSGLRQSLKFEDVKRL 365
           + +   + SA M A+ P    +  YL + +    L   F  YA    LR ++   + + L
Sbjct: 303 LFDSVCLCSADMYAIDPGKYFERRYLFYFL----LTDAFTAYAELESLRVAMPKVNREAL 358

Query: 366 PVLVPPI---KEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
              V PI    EQ +I +  +          +++++S+  L+E RS+ I AAVTGQI
Sbjct: 359 GAFVLPIPFLDEQTEIADYCSRVDRENRFAADEVKRSVQKLEEYRSALITAAVTGQI 415



 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 91/203 (44%), Gaps = 6/203 (2%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESG---KDIIYIGLEDVESGTGKYLPKD 67
           K SG+ W+G IP HW +VP K   ++ +G+         D+  I  + +ESGTG+     
Sbjct: 211 KPSGIDWLGDIPAHWDLVPFKWRCQVQSGQVDPREPEYTDMPLIAPDYIESGTGRLYDVP 270

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP-ELLQG 126
               Q   S     ++G +LY K+ P LRK  + D   +CS     + P        L  
Sbjct: 271 SAEEQGAISGKYFCSEGSVLYSKIRPALRKVALFDSVCLCSADMYAIDPGKYFERRYLFY 330

Query: 127 WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
           +LL+   T   E       M   + + +G   +PIP L EQ  I +   +   R +    
Sbjct: 331 FLLTDAFTAYAELESLRVAMPKVNREALGAFVLPIPFLDEQTEIAD-YCSRVDRENRFAA 389

Query: 187 ERI-RFIELLKEKKQALVSYIVT 208
           + + R ++ L+E + AL++  VT
Sbjct: 390 DEVKRSVQKLEEYRSALITAAVT 412


>gi|15839311|ref|NP_299999.1| type I restriction-modification system specificity determinant
           [Xylella fastidiosa 9a5c]
 gi|9187842|gb|AAF85758.1|AE004078_10 type I restriction-modification system specificity determinant
           [Xylella fastidiosa 9a5c]
          Length = 468

 Score =  103 bits (258), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 106/439 (24%), Positives = 191/439 (43%), Gaps = 34/439 (7%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG-LEDVESGTGKYLP 65
           YP Y+   ++W+ A+P+HW     K F +    R+    ++++ +  L  V S + K + 
Sbjct: 8   YPNYRQPKMRWLPAVPEHWNEQRAKTFFREVDERSKTGQEELLSVSHLTGVTSRSQKNVT 67

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV------ 119
                + +      +   G I+   L  ++     +   GI S  + V +P         
Sbjct: 68  M---FKAASYVGSKLCRPGDIVINTLWAWMAALGASRHVGIVSPAYGVYRPHHADSFNPA 124

Query: 120 -LPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
            L  LL+      +   R   I       + +     +I +  PP  EQ  I   +  + 
Sbjct: 125 YLDYLLRTRAYVAEYIGRSTGIRSSRLRLYPN--QFLDIALIQPPRPEQDQIVAYLRVQD 182

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
             I   I  +   I+LL E+K+ ++ + VT+GL+  V +K SGIEW+G VP HW+VKP  
Sbjct: 183 AHIARFIKVKRDLIKLLTEQKRRIIDHAVTRGLDASVALKPSGIEWLGDVPVHWDVKPLK 242

Query: 239 ALV----TELNRKNTKLIE---SNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEI 291
             V    + L  K     E    +I S+  G + ++LE     + P      +++  G+ 
Sbjct: 243 RWVRLNASTLGEKTDPDFEFRYVDIGSVQTGRLAKELERIRFEVAPS--RARRVLRRGDT 300

Query: 292 VFRFIDLQNDKRSLRS----AQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVF 346
           +   +     +  L++    ++  +  I ++ +  + P +  +  YL ++++S       
Sbjct: 301 IISTV-----RTYLKAIWYVSEEADDLIASTGFAVLTPGNSAEPEYLGYVIQSSAFVNRV 355

Query: 347 YAMGSGLRQSLKFEDV-KRLPVLVPP-IKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            A   G+      E V  R PV +PP + EQ  I   I  E+A +D  + + E+ I L++
Sbjct: 356 AANSIGIAYPAIAETVLGRFPVALPPTVDEQQAIVAHIKTESAPLDDAITRTEEEITLIR 415

Query: 405 ERRSSFIAAAVTGQIDLRG 423
           E R   I   VTGQ+D+RG
Sbjct: 416 EYRDRLITDVVTGQVDVRG 434


>gi|331084240|ref|ZP_08333345.1| hypothetical protein HMPREF0992_02269 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330401775|gb|EGG81352.1| hypothetical protein HMPREF0992_02269 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 456

 Score =  103 bits (257), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 78/275 (28%), Positives = 134/275 (48%), Gaps = 26/275 (9%)

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           +PP  EQ  I + +  +T  I+  I ++ + I+LL+E K   ++ +VTKGL  +VK K S
Sbjct: 162 VPPKPEQDKIVQFLEWKTSEINRFIHQKKKQIKLLEELKLTRINNLVTKGLTHNVKYKQS 221

Query: 221 GIEWVGLVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
            +EW+G +P+HW+V   K  F +   +  K       ++LS++   I +K  + N G   
Sbjct: 222 NVEWLGEIPEHWDVDYIKQHFKVKKRIAGKEG----YDVLSITQQGIKKKDISSNEGQMA 277

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLM 337
           +SY  YQ V  G+     +DL      + S Q    G+ +  Y        +  +  + +
Sbjct: 278 QSYANYQFVYSGDFAMNHMDLLTGYIDI-SKQF---GVTSPDYRVFNLSDSEHCFAPFYL 333

Query: 338 RSYDLC---KVFYAMGSGLRQSLKFEDVKRLPVL--------VPPIKEQFDITNVINVET 386
           R + +    K+FY  G G     ++    RLP+         VPPI EQ +I    +   
Sbjct: 334 RVFQIGYKRKIFYKFGKGAANQGRW----RLPITAFYDYAIQVPPIDEQREIARQCDEVE 389

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            +I+ ++  I + I L++E R+  I+  VTGQ+D+
Sbjct: 390 KQINEMISGINKEITLVEELRTKLISDVVTGQVDV 424



 Score = 83.2 bits (204), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 107/207 (51%), Gaps = 10/207 (4%)

Query: 216 KMKDSGIEWVGLVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRN 272
           K K+SGI W    P  W+    K  F     +N+ N      N+LSL+   +I+      
Sbjct: 7   KYKESGIPWEICEPTTWDCVRGKALFENPKYINKNNEY---KNVLSLTLKGVIRNNIENP 63

Query: 273 MGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV---KPHGID 329
            GL P SY+TYQ+ +  ++VF+ IDL+N   S R   V E+GI++ AY+ +   K    +
Sbjct: 64  NGLVPRSYDTYQLFEKDDLVFKLIDLENISTS-RVGIVGEQGIMSPAYIRLVLRKKEKQN 122

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
             Y  +   S    ++F ++G+G+RQ+L   ++    ++VPP  EQ  I   +  +T+ I
Sbjct: 123 IKYYYYQYFSLYQRQIFNSLGAGVRQTLSARELLEQKIMVPPKPEQDKIVQFLEWKTSEI 182

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVT 416
           +  + + ++ I LL+E + + I   VT
Sbjct: 183 NRFIHQKKKQIKLLEELKLTRINNLVT 209



 Score = 42.7 bits (99), Expect = 0.100,   Method: Compositional matrix adjust.
 Identities = 52/222 (23%), Positives = 93/222 (41%), Gaps = 22/222 (9%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           +YK S V+W+G IP+HW V  IK+  K+      + G D++ I     + G  K   KD 
Sbjct: 217 KYKQSNVEWLGEIPEHWDVDYIKQHFKVKKRIAGKEGYDVLSI----TQQGIKK---KDI 269

Query: 69  NSRQSDTSTVSIFAKGQILY-GKLGPYLRKAIIADFD-----GICSTQFLVLQPKDVLPE 122
           +S +   +    +A  Q +Y G         +    D     G+ S  + V    D    
Sbjct: 270 SSNEGQMAQS--YANYQFVYSGDFAMNHMDLLTGYIDISKQFGVTSPDYRVFNLSDSEHC 327

Query: 123 LLQGWL--LSIDVTQRIEAICEGATMSHADWK----GIGNIPMPIPPLAEQVLIREKIIA 176
               +L    I   ++I         +   W+       +  + +PP+ EQ  I  +   
Sbjct: 328 FAPFYLRVFQIGYKRKIFYKFGKGAANQGRWRLPITAFYDYAIQVPPIDEQREIARQCDE 387

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLN-PDVKM 217
              +I+ +I+   + I L++E +  L+S +VT  ++  DVK+
Sbjct: 388 VEKQINEMISGINKEITLVEELRTKLISDVVTGQVDVSDVKI 429


>gi|283796106|ref|ZP_06345259.1| putative type I restriction enzyme specificity protein [Clostridium
           sp. M62/1]
 gi|291076320|gb|EFE13684.1| putative type I restriction enzyme specificity protein [Clostridium
           sp. M62/1]
          Length = 435

 Score =  103 bits (257), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 83/316 (26%), Positives = 157/316 (49%), Gaps = 24/316 (7%)

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           VL + +  + L    T ++E      T  +     +GN+ + +P   EQ  I + +  E 
Sbjct: 121 VLQKFIYYYSLCYSFTHQVEQSWSYGTQQNIGMGVLGNLYVTLPSSNEQQSIVDYLDKEC 180

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF 238
            +ID++  +  + I LL++ K++L++  VTKGL+  V MKDSG+EW+G +P+HW+V+P  
Sbjct: 181 AQIDSIAADLEKQIALLQQYKKSLITETVTKGLDKSVPMKDSGVEWIGKIPEHWDVEPIK 240

Query: 239 ALVTELNR-------KNTKLIESNILSLSYGNII-QKLETRNMGLKPESYETYQIVD--- 287
             VT  N          ++L    I  ++ G++    L   NM    E  E Y+I+    
Sbjct: 241 YRVTFHNGDRGENYPSKSELQSEGIPFINAGHLEGDGLNMDNMDYISE--EKYRIMGGVK 298

Query: 288 --PGEIVFRFIDLQNDKRSLRSAQV--MERGIITSAYMAVKPHGIDSTYLAWLMRSYDLC 343
             PG+I++        + S+    +  M +G + S+ +A++   I + YL + + S+   
Sbjct: 299 LRPGDILYCL------RGSVGKNAIVDMNQGTVASSLVAIRSVRILAEYLYYCLNSHIEE 352

Query: 344 KVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
              Y   +G  Q +L  +++ +    +PP++EQ  I   +N   ++ID LV   ++ +  
Sbjct: 353 VQRYLWDNGTAQPNLSADNLGKYKFCIPPVEEQKAIVKYLNNICSQIDNLVIGKKKQLST 412

Query: 403 LKERRSSFIAAAVTGQ 418
           +++ + S I   VTG+
Sbjct: 413 IQQHKKSLIYEYVTGK 428



 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 55/208 (26%), Positives = 89/208 (42%), Gaps = 11/208 (5%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG-N 69
           KDSGV+WIG IP+HW V PIK     + G   E+      +  E +      +L  DG N
Sbjct: 220 KDSGVEWIGKIPEHWDVEPIKYRVTFHNGDRGENYPSKSELQSEGIPFINAGHLEGDGLN 279

Query: 70  SRQSDTSTVSIF--------AKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
               D  +   +          G ILY   G   + AI+    G  ++  + ++   +L 
Sbjct: 280 MDNMDYISEEKYRIMGGVKLRPGDILYCLRGSVGKNAIVDMNQGTVASSLVAIRSVRILA 339

Query: 122 ELLQGWLLS-IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
           E L   L S I+  QR      G    +     +G     IPP+ EQ  I + +     +
Sbjct: 340 EYLYYCLNSHIEEVQRY-LWDNGTAQPNLSADNLGKYKFCIPPVEEQKAIVKYLNNICSQ 398

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVT 208
           ID L+  + + +  +++ K++L+   VT
Sbjct: 399 IDNLVIGKKKQLSTIQQHKKSLIYEYVT 426


>gi|259910155|ref|YP_002650511.1| putative type I restriction-modification system specificity subunit
           [Erwinia pyrifoliae Ep1/96]
 gi|224965777|emb|CAX57309.1| putative type I restriction-modification system specificity subunit
           [Erwinia pyrifoliae Ep1/96]
 gi|283480261|emb|CAY76177.1| type I restriction-modification system specificity subunit [Erwinia
           pyrifoliae DSM 12163]
          Length = 300

 Score =  103 bits (257), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 81/266 (30%), Positives = 131/266 (49%), Gaps = 34/266 (12%)

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           +T  ID  I  + + I LLKE+KQ ++   VT+GL+ +V  KDSG+ W+G +P+HWE++ 
Sbjct: 48  KTSEIDEAIAIKEKQISLLKERKQIIIQKAVTQGLDANVPRKDSGVSWIGKIPEHWEIRR 107

Query: 237 FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFI 296
              L T+   K            +  + +Q   T+  G+ P+  E Y+ +    +V   I
Sbjct: 108 SKFLFTQRKEK------------ALNDDVQLSATQAYGVIPQ--EKYEALTGKRVV--KI 151

Query: 297 DLQNDKR----------SLRSAQ-VMER----GIITSAYMAVKP-HGIDSTYLAWLMRSY 340
               DKR          S+RS Q  +ER    G I S+Y+ +K    ID  +  +L++  
Sbjct: 152 QFHLDKRKHVEKDDFVISMRSFQGGLERAWSCGCIRSSYVVLKALQTIDPLFYGYLLKLP 211

Query: 341 DLCKVFYAMGSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
                     S +R  Q L F++  R+ + +PP++EQ  I N +       D  +  IEQ
Sbjct: 212 SYIAALQQTASFIRDGQDLNFDNFSRVDLFIPPLEEQTAIANYVESFLTSSDEAMNLIEQ 271

Query: 399 SIVLLKERRSSFIAAAVTGQIDLRGE 424
            I  LKE +++ I +AVTG+I +  E
Sbjct: 272 QIEKLKEYKTTLINSAVTGKIKITPE 297



 Score = 46.2 bits (108), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 91/219 (41%), Gaps = 39/219 (17%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGL---------EDVESGTG 61
           KDSGV WIG IP+HW+   I+R   L T R  ++  D + +           E  E+ TG
Sbjct: 89  KDSGVSWIGKIPEHWE---IRRSKFLFTQRKEKALNDDVQLSATQAYGVIPQEKYEALTG 145

Query: 62  K-------YLPKDGNSRQSD-TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV 113
           K       +L K  +  + D   ++  F  G          L +A      G   + ++V
Sbjct: 146 KRVVKIQFHLDKRKHVEKDDFVISMRSFQGG----------LERAWSC---GCIRSSYVV 192

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATM----SHADWKGIGNIPMPIPPLAEQVL 169
           L+    +  L  G+LL +     I A+ + A+        ++     + + IPPL EQ  
Sbjct: 193 LKALQTIDPLFYGYLLKL--PSYIAALQQTASFIRDGQDLNFDNFSRVDLFIPPLEEQTA 250

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           I   + +     D  +    + IE LKE K  L++  VT
Sbjct: 251 IANYVESFLTSSDEAMNLIEQQIEKLKEYKTTLINSAVT 289


>gi|91776956|ref|YP_546712.1| restriction modification system DNA specificity subunit
           [Methylobacillus flagellatus KT]
 gi|91710943|gb|ABE50871.1| restriction modification system DNA specificity domain
           [Methylobacillus flagellatus KT]
          Length = 429

 Score =  102 bits (255), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 99/366 (27%), Positives = 162/366 (44%), Gaps = 35/366 (9%)

Query: 79  SIFAKGQILYGKLGPYLRKAIIADFDGI------CSTQFLVLQPKDVLPELLQGWLLSID 132
           + FA G +   K+ P       A  +G+       +T+  VL+P   LP L   +L  + 
Sbjct: 69  TYFADGDVCIAKITPCFENGKGAIAEGLKNGVAFGTTELHVLRP---LPTLDARFLFYLT 125

Query: 133 VTQRIEAICEGATMSHADWKGI-----GNIPMPIPPLAEQVLIREKIIAETVRIDTLITE 187
           +     +  E   +     K +      +   P+P +  Q  I   +  +T +ID LI +
Sbjct: 126 IAHDFRSHGESEMLGAGGQKRVPEGFLKDWTPPLPCIQVQQRIARFLDEKTAQIDGLIEK 185

Query: 188 RIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRK 247
           +   ++ L EK+QAL++  VTKG+NPD  MK SGI+W+G +P HWEV+      T ++ +
Sbjct: 186 KRALLDRLAEKRQALITRAVTKGMNPDAPMKPSGIDWLGDIPAHWEVRGLTKCTTRVDYR 245

Query: 248 NT--KLIESNILSLSYGNIIQKLETRNMGLK--PES-YETYQ---IVDPGEIVFRFIDLQ 299
               +   S +  ++  NI        +  +  PE  YE      +   GE++F      
Sbjct: 246 GATPEKSSSGVFLVTAKNIKNGRIDYQISQEYIPEDIYEQAMRRGLPKLGEVLF------ 299

Query: 300 NDKRSLRSAQVMERGIITSAYMAVK-----PHGIDSTYLAWLMRSYDLCKVFYAMGSGLR 354
             +  L     ++R  I  A   +K     P  +++ YLA+ M S        +  +G  
Sbjct: 300 TTEAPLGEIAQVDREDIALAQRIIKFTTSTPE-LENDYLAYWMMSMPFQAQIQSRATGST 358

Query: 355 Q-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAA 413
              LK   +  LP L+PP  EQ DI + +     +ID +   I  S+    E R++ I A
Sbjct: 359 AVGLKASKIVDLPCLLPPKDEQKDIISQVRQSLMKIDEIETAISDSLEFKIEYRAALITA 418

Query: 414 AVTGQI 419
           AVTGQI
Sbjct: 419 AVTGQI 424



 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 97/214 (45%), Gaps = 24/214 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNT-----GRTSE-SGKDIIYIGLEDVESG----- 59
           K SG+ W+G IP HW+V   +  TK  T     G T E S   +  +  +++++G     
Sbjct: 216 KPSGIDWLGDIPAHWEV---RGLTKCTTRVDYRGATPEKSSSGVFLVTAKNIKNGRIDYQ 272

Query: 60  -TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
            + +Y+P+D   +        +   G++L+    P    A + D + I   Q  +++   
Sbjct: 273 ISQEYIPEDIYEQAMRRGLPKL---GEVLFTTEAPLGEIAQV-DREDIALAQ-RIIKFTT 327

Query: 119 VLPEL----LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
             PEL    L  W++S+    +I++   G+T        I ++P  +PP  EQ  I  ++
Sbjct: 328 STPELENDYLAYWMMSMPFQAQIQSRATGSTAVGLKASKIVDLPCLLPPKDEQKDIISQV 387

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
               ++ID + T     +E   E + AL++  VT
Sbjct: 388 RQSLMKIDEIETAISDSLEFKIEYRAALITAAVT 421


>gi|310778850|ref|YP_003967183.1| restriction modification system DNA specificity domain protein
           [Ilyobacter polytropus DSM 2926]
 gi|309748173|gb|ADO82835.1| restriction modification system DNA specificity domain protein
           [Ilyobacter polytropus DSM 2926]
          Length = 433

 Score =  101 bits (251), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 119/448 (26%), Positives = 211/448 (47%), Gaps = 48/448 (10%)

Query: 1   MKHYKAYPQYKD-SGVQWIGAIPKHWKVVPI-----KRFTKLNTGRTSES---GKDIIYI 51
           +K  K+Y  YK+    +++  IP+ W ++P      +R  K N      S    K II  
Sbjct: 2   IKEKKSYLNYKNIPWYEYVKEIPQDWNILPNIALFDERIKKKNNNEELLSVTISKGII-- 59

Query: 52  GLEDVESGTGKYLPKD-GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
              D+E+       KD  N  +S+   V I   G I Y K+  +      + + GI S  
Sbjct: 60  KQSDIEN------KKDISNEDKSNYKLVKI---GDIAYNKMRMWQGSVGYSQYRGIVSPA 110

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIE-----AICEGA-TMSHADWKGIGNIPMPIPPL 164
           ++VL+ K  +      +L   +            +C+    + + D+K + +I   +P +
Sbjct: 111 YIVLKSKLKINSKYFHYLYRTEYYSNYARRYSYGLCDDQLNLRYVDFKRMYSI---VPHI 167

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
             Q  I E +  +  + +  I ++ + IELLKE+K+ +++ +VTKGLN  VKM+DSG+EW
Sbjct: 168 EIQDKIVEYLETKEKQSNKFIEKQQKMIELLKEQKKTIINEVVTKGLNTLVKMQDSGVEW 227

Query: 225 VGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPES----Y 280
           +G VP HWE+K    +   +NR  T     N    S   ++ +  T + G   ES    +
Sbjct: 228 LGKVPKHWEIKKLKEMSDFVNRGTT----PNYTEKSDYKVVNQA-TFSKGYFDESSIRFH 282

Query: 281 ETYQI-VDPGEIVFRFIDLQNDKRSL--RSAQVMER-GI-ITSAYMAV----KPHGIDST 331
           +TY+I  + G++ ++ I L +    +  + A   E+ G+ +  +++ +    K   I   
Sbjct: 283 KTYKIEKEKGKLKYKDILLASTGGGVLGKVAIFTEKEGVYLADSHVTIIRDSKKRFIPEY 342

Query: 332 YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
              +   +Y+L   ++  GS  +  L+ E ++++ +  P +KEQ  I N I  +  +ID 
Sbjct: 343 LYYFYYVNYNLIDGYFGQGSTNQTELQREWLRQMYLPYPDLKEQKQIVNYIEKQNTKIDT 402

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQI 419
            + K E+ I L K+   S I   VTGQI
Sbjct: 403 TILKTEKEIELAKDYMESLIYNVVTGQI 430


>gi|158337895|ref|YP_001519071.1| hypothetical protein AM1_4782 [Acaryochloris marina MBIC11017]
 gi|158308136|gb|ABW29753.1| conserved hypothetical protein [Acaryochloris marina MBIC11017]
          Length = 133

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 51/108 (47%), Positives = 69/108 (63%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           +DS + W+  VP+HW V+     +   N KN       +LSLSYG I+ K + +  GL P
Sbjct: 11  QDSQVSWLNEVPNHWRVELGRNYLRPKNVKNIGNHVKTVLSLSYGKIVIKPKEKLHGLVP 70

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP 325
           ES+ETYQIV+PG+I+ R  DLQND+ SLR   V + GIITSAY+ + P
Sbjct: 71  ESFETYQIVEPGDIIVRATDLQNDRTSLRIGLVQDHGIITSAYLCLSP 118


>gi|52426224|ref|YP_089361.1| HsdS protein [Mannheimia succiniciproducens MBEL55E]
 gi|52308276|gb|AAU38776.1| HsdS protein [Mannheimia succiniciproducens MBEL55E]
          Length = 449

 Score =  100 bits (250), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 114/467 (24%), Positives = 196/467 (41%), Gaps = 73/467 (15%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT--SESGKDIIYIGLEDVESGTGK 62
           + Y +YK SGV+W+G +P+ W+V  IK   +L   ++  +E  K+  ++ +E ++ G   
Sbjct: 2   QKYDKYKPSGVEWLGDVPEGWEVTKIKYIAELTPKKSELTELDKECSFVPMEKLKLGN-- 59

Query: 63  YLPKDGNSRQSDT-STVSIFAKGQILYGKLGPYL--RKAIIA----DFDGICSTQFLVLQ 115
            L  D     SD  +  + F    +L  K+ P    +  +IA    +  G  S++  VL+
Sbjct: 60  -LVLDETRTISDVYNGYTYFEDNDLLIAKVTPCFENKNFVIAEKLVNGIGFGSSEIYVLR 118

Query: 116 PKDVLPELLQGWLLS---IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
            K+ L   L   L     +D+   I ++     +     + + N  + +PPL EQ  I  
Sbjct: 119 VKNCLNRYLFYRLQENTFMDLA--IGSMTGAGGLKRIPSEFLNNYSIALPPLEEQTAIAH 176

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT------------------------ 208
            +  +T  ID LI  +   +E L EK+ AL++  V                         
Sbjct: 177 YLDQKTAYIDRLIDRQQTLLEKLSEKRTALITEAVCGRLPIAPYSASLKRGTGFDEENGS 236

Query: 209 ------------KGLNPDVKMKDSGIEWVGLVPDHWEV-KPFFALVTELNRKNTKLIESN 255
                       +GL  ++ +KDSGI+W+G VP+ WEV +  F    +    +T+  E +
Sbjct: 237 PNTAQTAPLFSKEGLG-EICLKDSGIQWLGKVPEGWEVIRLRFLCNIQTGNMDTQDNEPD 295

Query: 256 ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPG---EIVFRFIDLQNDKRSLRSAQVME 312
            +   Y  +   +  R+     E  E   +   G     VF ++               +
Sbjct: 296 GIYPFY--VRSPIIERSNNYTFEDDEAVLMAGDGVGAGKVFHYVQ-------------GK 340

Query: 313 RGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPI 372
            G     Y   +   I   +L + +R +   K+          S++   +K  P  VPP+
Sbjct: 341 YGCHQRVYSLNQFQNITGRFLFYYLREFFSRKIEEGGAKSTVDSVRLPMLKDFPTCVPPL 400

Query: 373 KEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
            EQ  IT+ ++ ETA+ID L  +IE  I  LKE R + I   VTG++
Sbjct: 401 SEQTTITHYLDQETAKIDRLRTQIETVIERLKEYRMALITQVVTGKV 447


>gi|315446766|ref|YP_004079645.1| restriction endonuclease S subunit [Mycobacterium sp. Spyr1]
 gi|315265069|gb|ADU01811.1| restriction endonuclease S subunit [Mycobacterium sp. Spyr1]
          Length = 411

 Score = 99.8 bits (247), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 85/314 (27%), Positives = 154/314 (49%), Gaps = 33/314 (10%)

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
            L  +L+++  +  IE  C   +M H   + +  +P+P+P  ++Q  I + +  ET RID
Sbjct: 117 FLAYYLIALRASGFIERYCNIVSMPHLTAEKLAALPVPVPDRSDQCAIADFLDRETARID 176

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
           TLI E+  F+ LL+E++QA++               DS +  V   P   +++    LVT
Sbjct: 177 TLIAEQQLFVGLLRERRQAVI---------------DSTVSVVKAEP--VQLRRVIELVT 219

Query: 243 ELNRK-NTKLIESNILSLSYGNIIQ-----KLETRNMGLKPESYE---TYQIVDPGEIVF 293
             +R       ++ +  L  GN+ +     + E + + L P+  E   T  +V  G+++F
Sbjct: 220 SGSRGWGDYYSDAGVRFLRIGNLPRTDLAIRGEVQLVDLPPDVTEGERTRLVV--GDVLF 277

Query: 294 RFIDLQNDKRSLRSAQVMERGIITS--AYMAVKPHGIDSTYLAWLMRSYD-LCKVFYAMG 350
                      +  A   E G ++   A   + P   +S ++ W+M + D   ++     
Sbjct: 278 SITAYLGSVAVVDDA--WEGGYVSQHVALCRLDPLRANSRFVGWVMLTTDGQDQLRQGAA 335

Query: 351 SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
            G +Q L  +D++ L V +P + EQ  I   ++ +T++ID L+ + +  I L +ERR++ 
Sbjct: 336 GGTKQQLGLDDIRELRVPLPLLDEQHRIVAFLDEQTSKIDTLIAETKVFIELSRERRTAL 395

Query: 411 IAAAVTGQIDLRGE 424
           I AAVTGQID+R E
Sbjct: 396 ITAAVTGQIDVRNE 409


>gi|201067913|ref|ZP_03217796.1| putative type I restriction-modification [Campylobacter jejuni
           subsp. jejuni BH-01-0142]
 gi|200004510|gb|EDZ04991.1| putative type I restriction-modification [Campylobacter jejuni
           subsp. jejuni BH-01-0142]
          Length = 269

 Score = 99.4 bits (246), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/283 (29%), Positives = 140/283 (49%), Gaps = 34/283 (12%)

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           M  PPL EQ  I   +  +  +I   I ++ + + LLKE+KQA ++   TKGL+ +V  K
Sbjct: 1   MLFPPLKEQEQIANFLDEKCKKIANFIEKKEKLMTLLKEQKQAFINKATTKGLDKNVNFK 60

Query: 219 DSGIEWVGLVPDHWEVKPFFALV-----TELNRKNTKLIE-SNILSLSYGNIIQKLETRN 272
           DSGIE++G +P HW++     ++     T  +  N K  +   I+ ++ G++       N
Sbjct: 61  DSGIEYLGEIPQHWKLVRLGLILKTSSGTTPDSGNDKYYKGGQIVWINSGDL-------N 113

Query: 273 MGLKPESYE--TYQIVDPGEIVFRFIDLQNDKRSL----------RSAQVMERGIITSAY 320
            G   +S    T   +D   ++  F     DK SL          ++A +     +  A 
Sbjct: 114 DGFLKDSKRKITQDALDDYSVLKIF-----DKDSLIVAMYGATIGKTAILKVNACVNQAC 168

Query: 321 MAV-KPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFED-VKRLPVLVPPIKEQFDI 378
             + K    ++ YL +L   Y   K   +MGSG  Q    +D +K + + +PP+KEQ  I
Sbjct: 169 CVLEKSAWYNTFYLFYLFNRYK--KELISMGSGGGQPNISQDIIKNIKIPLPPLKEQEQI 226

Query: 379 TNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            N ++ +  +ID+L+EK E+ I L+KE + +    AV G+I+L
Sbjct: 227 ANFLDEKCKKIDLLIEKTEKQIKLIKEYKITLTNQAVCGRINL 269



 Score = 73.2 bits (178), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 96/214 (44%), Gaps = 13/214 (6%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
            +KDSG++++G IP+HWK+V +    K ++G T +SG D  Y G + V   +G     DG
Sbjct: 58  NFKDSGIEYLGEIPQHWKLVRLGLILKTSSGTTPDSGNDKYYKGGQIVWINSGDL--NDG 115

Query: 69  NSRQS----------DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
             + S          D S + IF K  ++    G  + K  I   +  C  Q   +  K 
Sbjct: 116 FLKDSKRKITQDALDDYSVLKIFDKDSLIVAMYGATIGKTAILKVNA-CVNQACCVLEKS 174

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
                   + L     + + ++  G    +     I NI +P+PPL EQ  I   +  + 
Sbjct: 175 AWYNTFYLFYLFNRYKKELISMGSGGGQPNISQDIIKNIKIPLPPLKEQEQIANFLDEKC 234

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLN 212
            +ID LI +  + I+L+KE K  L +  V   +N
Sbjct: 235 KKIDLLIEKTEKQIKLIKEYKITLTNQAVCGRIN 268


>gi|168362839|ref|ZP_02696013.1| probable type I restriction-modification system [Ureaplasma
           urealyticum serovar 13 str. ATCC 33698]
 gi|171903131|gb|EDT49420.1| probable type I restriction-modification system [Ureaplasma
           urealyticum serovar 13 str. ATCC 33698]
          Length = 453

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 110/444 (24%), Positives = 198/444 (44%), Gaps = 50/444 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +Y+D+G+ WI  +PK W +  I      +  R   S KD  Y+ L   ++G  K L  
Sbjct: 4   YERYRDTGLIWINKVPKKWNLQKINAV--FDERREKVSDKD--YVALSVTKNGIFKQLDN 59

Query: 67  -----DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
                DG++R+       +        G  G       ++ FDG  S    VL+ K   P
Sbjct: 60  VAKTIDGDNRKKVKINDFVINSRSDRKGSSG-------LSRFDGSVSLINTVLKIKKEYP 112

Query: 122 ELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKI---IA 176
             +   L S+   +      +G  A +   +++ + +I +PIPP+ EQV I   +   I 
Sbjct: 113 RYMHYLLKSVPFQEEFYRNGKGIVADLWSTNFQSMKSIILPIPPIEEQVQIANYLDWKIN 172

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           E  R+  +  E+I+ +E L+     ++S  V +G+      K S I W+  +P HW    
Sbjct: 173 EINRLIQIEKEKIKELETLRFN---VISEFVLRGIGTQ-NYKKSSINWLDEIPSHWNEVS 228

Query: 237 FFALVTELNRKNTKLIESNI------LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
               V  + R N+   + ++      + L YG + +   T  +  + + Y + +   P +
Sbjct: 229 IRWCVNII-RGNSTFTKDDLQNRGKYVGLQYGKVYK---TEIIDSEFDFYVSDKFYKPAQ 284

Query: 291 IVFR----FIDLQNDKRSLRSAQVMER---GIITSAYMAVKP-HGIDSTYLAWLMRSYDL 342
           +V R     +        L      +R   G+I    + +KP + I+S YL +L + + +
Sbjct: 285 VVNRNDIIIVSTSETVEDLGHTSFYDRDDIGLIGGEQILLKPSNNINSKYLFYLSKIFRM 344

Query: 343 CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
                A G  + +  K  D+K++ V +PP+KEQ  I + I ++  +ID   E+++ +   
Sbjct: 345 QLQLCATGIKVYR-FKISDLKQIYVPLPPMKEQEKIVSNIELKLEQID---ERVKNNYAF 400

Query: 403 LKER---RSSFIAAAVTGQIDLRG 423
           +KE    + S I+  VTG+ID+R 
Sbjct: 401 IKELELLKQSLISEVVTGKIDVRN 424



 Score = 47.0 bits (110), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 96/216 (44%), Gaps = 16/216 (7%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           +N   + +D+G+ W+  VP  W ++   A+  E  R+     +   LS++   I ++L+ 
Sbjct: 1   MNKYERYRDTGLIWINKVPKKWNLQKINAVFDE-RREKVSDKDYVALSVTKNGIFKQLDN 59

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDS 330
               +  ++ +  +I D       F+      R   S      G ++     +K      
Sbjct: 60  VAKTIDGDNRKKVKIND-------FVINSRSDRKGSSGLSRFDGSVSLINTVLKIKKEYP 112

Query: 331 TYLAWLMRSYDLCKVFYAMGSGLRQSL---KFEDVKRLPVLVPPIKEQFDITNVINVETA 387
            Y+ +L++S    + FY  G G+   L    F+ +K + + +PPI+EQ  I N ++ +  
Sbjct: 113 RYMHYLLKSVPFQEEFYRNGKGIVADLWSTNFQSMKSIILPIPPIEEQVQIANYLDWKIN 172

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            I+ L++  ++ I  L+  R + I+  V     LRG
Sbjct: 173 EINRLIQIEKEKIKELETLRFNVISEFV-----LRG 203


>gi|330941784|gb|EGH44533.1| hypothetical protein PSYPI_19973 [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 472

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 102/441 (23%), Positives = 193/441 (43%), Gaps = 30/441 (6%)

Query: 6   AYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLP 65
           AYP Y+   ++W+  +PKHW     K F +    R+    ++++ +      +G      
Sbjct: 6   AYPSYRQPKMRWLSTVPKHWNEQRAKTFFREVNERSKTGLEELLSVSHL---TGITPRSQ 62

Query: 66  KDGNSRQSDTSTVSIFAK-GQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV----- 119
           K+    ++ +   S   + G I+   L  ++     +  +GI S  + V +P        
Sbjct: 63  KNVTMFKAASYVGSKLCRPGDIVINTLWAWMAALGTSRHEGIVSPAYGVYRPHQADSFSP 122

Query: 120 --LPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
             L  LL+      +   R   I       + +     +I +  PP  EQ  I   + A+
Sbjct: 123 AYLDYLLRTRFYVAEYIGRSTGIRASRLRLYPN--QFLDIQLIQPPRPEQDQIVAYLRAQ 180

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF 237
              I   I  +   I+L+ E+K  ++ + VT GL+  V +K S +EW+G VP HWEV  F
Sbjct: 181 DAHIARFIKTKRDLIKLITEQKLHIIDHAVTGGLDASVALKPSDVEWLGEVPKHWEVA-F 239

Query: 238 FALVTELN----RKNTKLIESNILSLSYGNIIQKLE-TRNMGLKPESYETYQI----VDP 288
              +  ++     K++   E+ +   +Y ++ +    T +M L   +    +I    +  
Sbjct: 240 IKHIANVHFSGVDKHSHDDETPVRLCNYTDVYKNDRITDDMNLMRATATAAEIARLTLKA 299

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMER--GIITSAYMAV---KPHGIDSTYLAWLMRSYDLC 343
           G+++        D   +  A V E   G++ + ++ +    P  +   +L   + S    
Sbjct: 300 GDVILTKDSETPDDIGV-PAWVPEDLPGVVCAYHLGLLRPVPDRVLGEFLFRAIGSARTA 358

Query: 344 KVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
           + F+ + +G+ R +L   DVK   + +PP++EQ  I   I  E   ++ ++ + E  I L
Sbjct: 359 QQFHILATGVTRFALGKHDVKNAVIALPPVEEQQAICRWITDECRPLNDVIARTEDEIKL 418

Query: 403 LKERRSSFIAAAVTGQIDLRG 423
           ++E R   IA  VTGQ+D+RG
Sbjct: 419 IREYRDRLIADVVTGQVDVRG 439


>gi|303235367|ref|ZP_07321984.1| type I restriction modification DNA specificity domain protein
           [Finegoldia magna BVS033A4]
 gi|302493488|gb|EFL53277.1| type I restriction modification DNA specificity domain protein
           [Finegoldia magna BVS033A4]
          Length = 426

 Score = 97.1 bits (240), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 116/460 (25%), Positives = 191/460 (41%), Gaps = 92/460 (20%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-------SESGKDIIYIGLEDVESGTGKY 63
           KDSG++WIG IP+ W++   KR++K   G T         + K+ I +     E     Y
Sbjct: 6   KDSGIEWIGEIPEDWEISKFKRYSKSAMGNTILKTDLEENNNKETIPVYSATQEDVVFGY 65

Query: 64  LPKDGNSRQSDTSTVSIFAKGQ-ILYGKLGPYLRKA-----IIADFDGI-------CSTQ 110
           + ++  +     + + I A+G  I + KL PY +       I +  + I       CS  
Sbjct: 66  IDENNVTVILKKNNLVIPARGNSIGFTKLVPYAKATCTQTTIFSRLNNINEKFVYYCSIA 125

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           F     KD   E  Q  +  I V Q                  + N  +PI  + EQ  I
Sbjct: 126 F-----KDSWFEFDQTAIPQITVQQ------------------VENNNIPICSIEEQCKI 162

Query: 171 REKI---IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
              +   +     I  +IT +I   E L+  K+++++  VTKGL+ +V+MKDSGIEW+G 
Sbjct: 163 TNFLSNKLENVKNIKIIITNQI---ENLENYKKSVITEAVTKGLDKNVEMKDSGIEWIGK 219

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
           +P HWE+K         N KN  L      S SY     K +  N     + +      D
Sbjct: 220 IPKHWEIK---------NIKNLTLKSERGTSPSYIEDDTKSKVVNQATFSQGF-----FD 265

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVM----ERGIITSAYMAVKPHGIDSTYLA----WLMRS 339
              I +  I   N +  L+   V+      G++   +  ++    D  Y+A     ++R+
Sbjct: 266 KSNIKYSKIPTNNSRGLLKKGDVLIASTGGGVLGKTHFFIE----DGEYVADGHITILRT 321

Query: 340 -----------------YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVI 382
                            Y+L     A GS  +  L+ E +K   V   PI+EQ  I N +
Sbjct: 322 DSLEQNSKILYYIFSVNYELINGILAKGSTNQTELQSEWLKSFKVPYAPIEEQIRIVNYL 381

Query: 383 NVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           + +   ID  +   ++ +  L+E + S I   VTG+ +++
Sbjct: 382 DEKCKLIDDSISLKKKQLETLEEYKKSLIYEYVTGKKEVK 421



 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 51/228 (22%), Positives = 95/228 (41%), Gaps = 48/228 (21%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           + KDSG++WIG IPKHW++  IK  T  +   TS S                  Y+  D 
Sbjct: 208 EMKDSGIEWIGKIPKHWEIKNIKNLTLKSERGTSPS------------------YIEDDT 249

Query: 69  NSRQSDTSTVS--IFAKGQILYGKLGPYLRKAIIADFD--------GICSTQFLVLQPKD 118
            S+  + +T S   F K  I Y K+     + ++   D        G+       ++  +
Sbjct: 250 KSKVVNQATFSQGFFDKSNIKYSKIPTNNSRGLLKKGDVLIASTGGGVLGKTHFFIEDGE 309

Query: 119 VLPE----------LLQG-----WLLSIDVTQRIEAICEGATMS---HADWKGIGNIPMP 160
            + +          L Q      ++ S++       + +G+T      ++W  + +  +P
Sbjct: 310 YVADGHITILRTDSLEQNSKILYYIFSVNYELINGILAKGSTNQTELQSEW--LKSFKVP 367

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             P+ EQ+ I   +  +   ID  I+ + + +E L+E K++L+   VT
Sbjct: 368 YAPIEEQIRIVNYLDEKCKLIDDSISLKKKQLETLEEYKKSLIYEYVT 415



 Score = 40.4 bits (93), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 14/22 (63%), Positives = 18/22 (81%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPF 237
           KMKDSGIEW+G +P+ WE+  F
Sbjct: 4   KMKDSGIEWIGEIPEDWEISKF 25


>gi|269123432|ref|YP_003306009.1| restriction modification system DNA specificity domain-containing
           protein [Streptobacillus moniliformis DSM 12112]
 gi|268314758|gb|ACZ01132.1| restriction modification system DNA specificity domain protein
           [Streptobacillus moniliformis DSM 12112]
          Length = 473

 Score = 97.1 bits (240), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 108/449 (24%), Positives = 201/449 (44%), Gaps = 40/449 (8%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGKYLP 65
           Y +Y +S + W  AIP+HW V  I R   +   + S    K+I+ +  +   S       
Sbjct: 4   YEKYSNSELTWSEAIPEHWGVKRIARVFDIRKEKNSPIKTKEILSLSAKHGVSLYSDKKE 63

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQF--LVLQPKDVLPEL 123
           K GN  + D ++ ++   G IL   +        I+++ G  S  +  LV   +D     
Sbjct: 64  KGGNKPKEDLTSYNLCYLGDILINCMNVVAGSVGISNYFGAVSPVYYPLVNMNQDENGTR 123

Query: 124 LQGWLL-SIDVTQRIEAICEGATMSHAD------------WKGIGNIPMPIPPLAEQVLI 170
              ++  + +  + +  + +G  MS AD            W  +    +PIPP+ EQ  I
Sbjct: 124 YMEYVFRNYNFQRSLVGLGKGIQMSEADDGRLYTVRMRISWDILKTQLLPIPPINEQEQI 183

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              +  +   ID LI      I+ LK     +++  V KG+N  +  K S I+W+  +P 
Sbjct: 184 ANYLDWKINEIDRLIQIEKEKIKELKRLTLNIIAEFVLKGINT-LNYKKSNIKWIDNIPS 242

Query: 231 HWEVKPFFALVTELNRKNTKLIESNI------LSLSYGNIIQK--LETR-NMGLKPESYE 281
           HW        V  + R N+   + ++      + L YG + +   +++  N  +  + Y+
Sbjct: 243 HWNEISIRGCVNII-RGNSSFTKDDLKNQGEYVGLQYGKVYKTEIIDSEFNFYVNDKFYK 301

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMER---GIITSAYMAVKP-HGIDSTYLAWLM 337
           T Q+V   +I+   +        L      +R   G+I    + +KP + I+S +L +L 
Sbjct: 302 TSQVVTRNDIII--VSTSETVEDLGHTSFYDRHDIGLIGGEQILLKPLNNINSKFLFYLS 359

Query: 338 RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
           + +       A G  + +  K  D+K+L + +PPI+EQ +I + I ++  ++D   E+++
Sbjct: 360 KIFRTQLQLCATGIKVYR-FKISDLKQLYIPLPPIEEQENIVSNIELKLKQLD---ERVK 415

Query: 398 QSIVLLKE---RRSSFIAAAVTGQIDLRG 423
            +  L+KE    + S I+  VTG+ID+R 
Sbjct: 416 NNYNLIKELELLKQSLISEVVTGKIDVRN 444



 Score = 48.1 bits (113), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 51/229 (22%), Positives = 98/229 (42%), Gaps = 23/229 (10%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS--YGNIIQKL 268
           +N   K  +S + W   +P+HW VK    +      KN+ +    ILSLS  +G  +   
Sbjct: 1   MNRYEKYSNSELTWSEAIPEHWGVKRIARVFDIRKEKNSPIKTKEILSLSAKHGVSLYSD 60

Query: 269 ETRNMGLKP-ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG 327
           +    G KP E   +Y +   G+I+   +++      + +      G ++  Y  +    
Sbjct: 61  KKEKGGNKPKEDLTSYNLCYLGDILINCMNVVAGSVGISNY----FGAVSPVYYPLVNMN 116

Query: 328 IDST---YLAWLMRSYDLCKVFYAMGSGLRQS-------------LKFEDVKRLPVLVPP 371
            D     Y+ ++ R+Y+  +    +G G++ S             + ++ +K   + +PP
Sbjct: 117 QDENGTRYMEYVFRNYNFQRSLVGLGKGIQMSEADDGRLYTVRMRISWDILKTQLLPIPP 176

Query: 372 IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           I EQ  I N ++ +   ID L++  ++ I  LK    + IA  V   I+
Sbjct: 177 INEQEQIANYLDWKINEIDRLIQIEKEKIKELKRLTLNIIAEFVLKGIN 225


>gi|162448114|ref|YP_001621246.1| type I restriction enzyme, S subunit [Acholeplasma laidlawii PG-8A]
 gi|161986221|gb|ABX81870.1| type I restriction enzyme, S subunit [Acholeplasma laidlawii PG-8A]
          Length = 437

 Score = 96.7 bits (239), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 118/240 (49%), Gaps = 27/240 (11%)

Query: 13  SGVQWI-GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY----IGLEDVESGTGKYLPKD 67
           + V +I G +P +WK + IK F +L +G T  S  D  Y    +   ++   T      D
Sbjct: 2   NDVNYIYGVVPDNWKKMKIKHFYELYSGGTPLSSVDSNYAEEGVCFVNISDMTNTEYITD 61

Query: 68  GNSRQSD----TSTVSIFAKGQILY------GKLGPYLRKAIIADFDGICSTQFLVLQPK 117
              + +D       + I   G ILY      G +     KA I       S   L L PK
Sbjct: 62  TTKKLTDKGIKNKNLKILKSGTILYSIYASLGSVSELKTKATI-------SQAILALIPK 114

Query: 118 ---DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
               +    L+ +LL I   + I     G T S+ +   + N+P+ IP L  Q+ I   +
Sbjct: 115 MGISIDKNYLK-FLLMI-AKENIFYFSNGTTQSNLNADIVNNLPLIIPELNNQIRISLYV 172

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             +T+ I+ LI  + + IE LKE KQ+L+S +VTKGLNP+V+ KDS ++W+GL+P +++V
Sbjct: 173 GNKTLIINKLIDNQKQQIEKLKEYKQSLISEVVTKGLNPNVEFKDSNVKWIGLIPKNYDV 232



 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 50/207 (24%), Positives = 97/207 (46%), Gaps = 25/207 (12%)

Query: 226 GLVPDHWE---VKPFFALV---TELNRKNTKLIESNILSLSYGNIIQKL----ETRNMGL 275
           G+VPD+W+   +K F+ L    T L+  ++   E  +  ++  ++         T+ +  
Sbjct: 9   GVVPDNWKKMKIKHFYELYSGGTPLSSVDSNYAEEGVCFVNISDMTNTEYITDTTKKLTD 68

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRS-AQVMERGIITSAYMAVKPH---GIDST 331
           K    +  +I+  G I++          SL S +++  +  I+ A +A+ P     ID  
Sbjct: 69  KGIKNKNLKILKSGTILYSIY------ASLGSVSELKTKATISQAILALIPKMGISIDKN 122

Query: 332 YLAWLMRSYDLCK--VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           YL +L+    + K  +FY      + +L  + V  LP+++P +  Q  I+  +  +T  I
Sbjct: 123 YLKFLLM---IAKENIFYFSNGTTQSNLNADIVNNLPLIIPELNNQIRISLYVGNKTLII 179

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVT 416
           + L++  +Q I  LKE + S I+  VT
Sbjct: 180 NKLIDNQKQQIEKLKEYKQSLISEVVT 206


>gi|255657323|ref|ZP_05402732.1| type I restriction-modification system [Clostridium difficile
           QCD-23m63]
          Length = 453

 Score = 96.3 bits (238), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 110/444 (24%), Positives = 197/444 (44%), Gaps = 50/444 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +Y+D+G+ WI  +PK W +  I      +  R   S KD  Y  L   ++G  K L  
Sbjct: 4   YERYRDTGLIWINKVPKKWNLQKINAV--FDERREKVSDKD--YEALSVTKNGIFKQLDN 59

Query: 67  -----DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
                DG++R+       +        G  G       ++ FDG  S    VL+ K   P
Sbjct: 60  VAKTIDGDNRKKVKINDFVINSRSDRKGSSG-------LSRFDGSVSLINTVLKIKKEYP 112

Query: 122 ELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKI---IA 176
             +   L S+   +      +G  A +   +++ + +I +PIPP+ EQV I   +   I 
Sbjct: 113 RYMHYLLKSVPFQEEFYRNGKGIVADLWSTNFQSMKSIILPIPPIEEQVQIANYLDWKIN 172

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
           E  R+  +  E+I+ +E L+     ++S  V +G+      K S I W+  +P HW    
Sbjct: 173 EINRLIQIEKEKIKELETLRFN---VISEFVLRGIGTQ-NYKKSSINWLDEIPSHWNEVS 228

Query: 237 FFALVTELNRKNTKLIESNI------LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
               V  + R N+   + ++      + L YG + +   T  +  + + Y + +   P +
Sbjct: 229 IRWCVNII-RGNSTFTKDDLQNRGKYVGLQYGKVYK---TEIIDSEFDFYVSDKFYKPAQ 284

Query: 291 IVFR----FIDLQNDKRSLRSAQVMER---GIITSAYMAVKP-HGIDSTYLAWLMRSYDL 342
           +V R     +        L      +R   G+I    + +KP + I+S YL +L + + +
Sbjct: 285 VVNRNDIIIVSTSETVEDLGHTSFYDRDDIGLIGGEQILLKPSNNINSKYLFYLSKIFRM 344

Query: 343 CKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVL 402
                A G  + +  K  D+K++ V +PP+KEQ  I + I ++  +ID   E+++ +   
Sbjct: 345 QLQLCATGIKVYR-FKISDLKQIYVPLPPMKEQEKIVSNIELKLEQID---ERVKNNYAF 400

Query: 403 LKER---RSSFIAAAVTGQIDLRG 423
           +KE    + S I+  VTG+ID+R 
Sbjct: 401 IKELELLKQSLISEVVTGKIDVRN 424



 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 96/216 (44%), Gaps = 16/216 (7%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           +N   + +D+G+ W+  VP  W ++   A+  E  R+     +   LS++   I ++L+ 
Sbjct: 1   MNKYERYRDTGLIWINKVPKKWNLQKINAVFDE-RREKVSDKDYEALSVTKNGIFKQLDN 59

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDS 330
               +  ++ +  +I D       F+      R   S      G ++     +K      
Sbjct: 60  VAKTIDGDNRKKVKIND-------FVINSRSDRKGSSGLSRFDGSVSLINTVLKIKKEYP 112

Query: 331 TYLAWLMRSYDLCKVFYAMGSGLRQSL---KFEDVKRLPVLVPPIKEQFDITNVINVETA 387
            Y+ +L++S    + FY  G G+   L    F+ +K + + +PPI+EQ  I N ++ +  
Sbjct: 113 RYMHYLLKSVPFQEEFYRNGKGIVADLWSTNFQSMKSIILPIPPIEEQVQIANYLDWKIN 172

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            I+ L++  ++ I  L+  R + I+  V     LRG
Sbjct: 173 EINRLIQIEKEKIKELETLRFNVISEFV-----LRG 203


>gi|255102540|ref|ZP_05331517.1| type I restriction-modification system [Clostridium difficile
           QCD-63q42]
          Length = 453

 Score = 95.9 bits (237), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 112/448 (25%), Positives = 195/448 (43%), Gaps = 58/448 (12%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y +Y+D+G+ WI  +PK W +  I      +  R   S KD  Y  L   ++G  K L  
Sbjct: 4   YERYRDTGLIWINKVPKKWNLQKINAV--FDERREKVSDKD--YEALSVTKNGIFKQLDN 59

Query: 67  -----DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
                DG++R+       +        G  G       ++ FDG  S    VL+ K   P
Sbjct: 60  VAKTIDGDNRKKVKINDFVINSRSDRKGSSG-------LSRFDGSVSLINTVLKIKKEYP 112

Query: 122 ELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
             +   L S+   +      +G  A +   +++ + +I +PIPP+ EQV I         
Sbjct: 113 RYMHYLLKSVPFQEEFYRNGKGIVADLWSTNFQSMKSIILPIPPIEEQVQIAN------- 165

Query: 180 RIDTLITERIRFIELLKEKKQAL-------VSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
            +D  I E  R I++ KEK + L       +S  V +G+      K S I W+  +P HW
Sbjct: 166 YLDWKINEINRLIQIEKEKIKELETLRFNAISEFVLRGIGTQ-NYKKSSINWLDEIPSHW 224

Query: 233 EVKPFFALVTELNRKNTKLIESNI------LSLSYGNIIQKLETRNMGLKPESYETYQIV 286
                   V  + R N+   + ++      + L YG + +   T  +  + + Y + +  
Sbjct: 225 NEVSIRWCVNII-RGNSTFTKDDLQNRGKYVGLQYGKVYK---TEIIDSEFDFYVSDKFY 280

Query: 287 DPGEIVFR----FIDLQNDKRSLRSAQVMER---GIITSAYMAVKP-HGIDSTYLAWLMR 338
            P ++V R     +        L      +R   G+I    + +KP + I+S YL +L +
Sbjct: 281 KPAQVVNRNDIIIVSTSETVEDLGHTSFYDRDDIGLIGGEQILLKPSNNINSKYLFYLSK 340

Query: 339 SYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
            + +     A G  + +  K  D+K++ V +PP+KEQ  I + I ++  +ID   E+++ 
Sbjct: 341 IFRMQLQLCATGIKVYR-FKISDLKQIYVPLPPMKEQEKIVSNIELKLEQID---ERVKN 396

Query: 399 SIVLLKER---RSSFIAAAVTGQIDLRG 423
           +   +KE    + S I+  VTG+ID+R 
Sbjct: 397 NYAFIKELELLKQSLISEVVTGKIDVRN 424



 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 96/216 (44%), Gaps = 16/216 (7%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           +N   + +D+G+ W+  VP  W ++   A+  E  R+     +   LS++   I ++L+ 
Sbjct: 1   MNKYERYRDTGLIWINKVPKKWNLQKINAVFDE-RREKVSDKDYEALSVTKNGIFKQLDN 59

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDS 330
               +  ++ +  +I D       F+      R   S      G ++     +K      
Sbjct: 60  VAKTIDGDNRKKVKIND-------FVINSRSDRKGSSGLSRFDGSVSLINTVLKIKKEYP 112

Query: 331 TYLAWLMRSYDLCKVFYAMGSGLRQSL---KFEDVKRLPVLVPPIKEQFDITNVINVETA 387
            Y+ +L++S    + FY  G G+   L    F+ +K + + +PPI+EQ  I N ++ +  
Sbjct: 113 RYMHYLLKSVPFQEEFYRNGKGIVADLWSTNFQSMKSIILPIPPIEEQVQIANYLDWKIN 172

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            I+ L++  ++ I  L+  R + I+  V     LRG
Sbjct: 173 EINRLIQIEKEKIKELETLRFNAISEFV-----LRG 203


>gi|149927743|ref|ZP_01915995.1| hypothetical protein LMED105_16098 [Limnobacter sp. MED105]
 gi|149823569|gb|EDM82799.1| hypothetical protein LMED105_16098 [Limnobacter sp. MED105]
          Length = 428

 Score = 95.9 bits (237), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 110/444 (24%), Positives = 192/444 (43%), Gaps = 55/444 (12%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNT----GRTSESGKDII-YIGLEDVESGTG 61
           YP+YK SG    G IP HW+   ++   +       G   + G+D I  I + D +  + 
Sbjct: 4   YPEYKSSGSPVFGDIPSHWEKKRLRDCIECCVNGIWGDEPDGGEDDIPVIRVADFDRPSR 63

Query: 62  KYLPKDGNSRQSDTSTVS-IFAKGQILYGKLGPYLRK--AIIADFDG----ICSTQFLVL 114
           K    +   +   T  V      G +L  K G   ++   ++  + G    +CS     +
Sbjct: 64  KVEKFETVRKVEKTQRVGRALYNGDMLIEKSGGGEQQPVGMVVSYQGPEGAVCSNFVAKM 123

Query: 115 QPKDVLPELLQGWL-----------LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
            PK+ +      +L           +SI  T  I+ +   A +S +         + +P 
Sbjct: 124 TPKENIASRFLVYLHSHLYASGVTNISIKQTTGIQNLDSTAYLSES---------IYVPS 174

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
           L EQV I + +  ET RIDTLI E+   I LL E KQ++   ++TKGL+ ++  K S +E
Sbjct: 175 LGEQVAIAQYLDIETARIDTLIYEKEALIGLLDEWKQSVTEQVLTKGLSANIDFKTSDVE 234

Query: 224 WV--GLVPDHW---EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPE 278
           W+    +P  W    +K    + +     +  + +S    +  GN ++   T     K  
Sbjct: 235 WLQGAEIPSQWVTKSIKHIAHMRSGETITSENIDDSGKYPVYGGNGLRGFTTE----KTH 290

Query: 279 SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMR 338
             E   I   G +      ++ +  +   A V+                IDS +  +++R
Sbjct: 291 DGEYLLIGRQGALCGNVHHVKGEFWATEHAVVVTLNT-----------DIDSRWAFYMLR 339

Query: 339 SYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
             DL +  Y++ +  +  L  E +  L + VP   EQ  I++ ++ E AR++ L+    +
Sbjct: 340 FMDLGQ--YSLAAA-QPGLSVEKIVGLKLPVPSCHEQKAISDHLDKEMARLEDLINHTTK 396

Query: 399 SIVLLKERRSSFIAAAVTGQIDLR 422
            I LL+E R++ IA AV G+ID+R
Sbjct: 397 EIELLRELRAATIADAVLGRIDVR 420


>gi|330469019|ref|YP_004406762.1| restriction modification system DNA specificity subunit
           [Verrucosispora maris AB-18-032]
 gi|328811990|gb|AEB46162.1| restriction modification system DNA specificity subunit
           [Verrucosispora maris AB-18-032]
          Length = 428

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 86/312 (27%), Positives = 144/312 (46%), Gaps = 20/312 (6%)

Query: 127 WLLSID---VTQRIEAICEGAT-MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
           WL ++    +T+R +      T + + D     N    +P L EQ  I + +  ET RID
Sbjct: 118 WLYALAASYLTRRTQKCVRQTTGIQNLDQGAFFNEVFAVPTLGEQRAIADYLDRETTRID 177

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
           TLI E+   IE+L+E++ AL  ++   G    V   +S + W   +P  W V P  ++  
Sbjct: 178 TLIEEQQHLIEMLRERRNALRVHVALHGTR-QVAEVESPLPWASKIPASWRVVPLTSVAQ 236

Query: 243 ELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIV--------FR 294
             +         +  +  Y   +   +   M      ++T Q +    I          R
Sbjct: 237 LESGHTPSRSREDWWTDCYIPWVSLHDVGAMRGTKYLHDTEQRISDAGIANSSARLLPAR 296

Query: 295 FIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVF--YAMG 350
            + L  D    R+A +M   + TS + A    G  +D  YL W++ +  +   F  +  G
Sbjct: 297 TVVLSRDATVGRTA-IMAVPMATSQHFAAWVCGPLLDPEYL-WVLFADAMQPFFDSFQNG 354

Query: 351 SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSF 410
           S +R ++   D+K   + +PP+ EQ  I   ++ ET +ID L+ + E+ I L +ERR++ 
Sbjct: 355 STIR-TIGMGDLKAFRIPLPPLDEQRRIVEYLDEETPKIDTLIVETERFIELARERRAAL 413

Query: 411 IAAAVTGQIDLR 422
           I AAVTGQID+R
Sbjct: 414 ITAAVTGQIDVR 425



 Score = 77.4 bits (189), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 100/214 (46%), Gaps = 16/214 (7%)

Query: 12  DSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-SESGKD------IIYIGLEDVESGTGKYL 64
           +S + W   IP  W+VVP+    +L +G T S S +D      I ++ L DV +  G   
Sbjct: 213 ESPLPWASKIPASWRVVPLTSVAQLESGHTPSRSREDWWTDCYIPWVSLHDVGAMRGTKY 272

Query: 65  PKDGNSRQSDT----STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL 120
             D   R SD     S+  +     ++  +     R AI+A      S  F       +L
Sbjct: 273 LHDTEQRISDAGIANSSARLLPARTVVLSRDATVGRTAIMA-VPMATSQHFAAWVCGPLL 331

Query: 121 -PELLQGWLLSIDVTQRI-EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
            PE L  W+L  D  Q   ++   G+T+       +    +P+PPL EQ  I E +  ET
Sbjct: 332 DPEYL--WVLFADAMQPFFDSFQNGSTIRTIGMGDLKAFRIPLPPLDEQRRIVEYLDEET 389

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLN 212
            +IDTLI E  RFIEL +E++ AL++  VT  ++
Sbjct: 390 PKIDTLIVETERFIELARERRAALITAAVTGQID 423


>gi|255308175|ref|ZP_05352346.1| putative type I site-specific restriction-modification system, S
           subunit [Clostridium difficile ATCC 43255]
          Length = 455

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 124/478 (25%), Positives = 208/478 (43%), Gaps = 89/478 (18%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYI---GLE--DVES 58
           Y+   + KDSGV+WIG IPK W+V  IK   +L   ++ E    ++ +   GL+  DV +
Sbjct: 5   YRDDEEMKDSGVEWIGKIPKDWEVKRIKHLFELKKDKSDEENPTVLSLTQKGLKIRDVSN 64

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGP------YLRKAIIADFDGICSTQFL 112
             G+             ST   + K +     L P      Y  KA I   +G+ S  + 
Sbjct: 65  NEGQL-----------ASTYVGYTKIEKNDFILNPMDLISGYTDKAEI---EGVISPAYT 110

Query: 113 VLQPKDVLPELLQGWLLSIDVTQRIEAIC----------EGATMSHADW----KGIGNIP 158
             + K+ +        ++ D  +R   +           EG +  H  W    +   N+P
Sbjct: 111 TFRSKNKVN-------INHDYYKRYFQMHYHHNFLFPWGEGVSFEHR-WTLKNEVFLNLP 162

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVS-------------- 204
           +    L EQ  I   +  +T + + +I+++   I+ L+E K++L+S              
Sbjct: 163 VITNRLEEQEKIANFLDEKTSQFEFIISKKEELIKKLEEAKKSLISEVVTGKVKVVKTDD 222

Query: 205 -YIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF---FALVTELNRKNTKLIESNILSLS 260
            Y + K  + +  MKDSGIEW+G +P  WEVK F   F L   L+     L ES I  ++
Sbjct: 223 GYKLVKRSSEE--MKDSGIEWLGEIPKDWEVKNFKYMFTLNKGLSITKADLKESGIPCVN 280

Query: 261 YGNIIQKLETRNMGLKP---------ESY---ETYQIVDPGEIVFRFIDLQNDKRSLRSA 308
           YG I  K       LKP         ESY    +  ++  G+ VF   D   D     + 
Sbjct: 281 YGEIHSKYR---FELKPSKHKLKYVDESYLKSNSISLLKYGDFVF--CDTSEDIEGCGNF 335

Query: 309 QVM-ERGIITSAY---MAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVK 363
             + E   + + Y   +A     ++  Y+++L  S D         SG++  S+    +K
Sbjct: 336 TYLNENNKVFAGYHTIIARTLEQVNYRYMSYLFDSNDWRIQIRTKVSGVKVFSITQSILK 395

Query: 364 RLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
              V++P + EQ +I   ++ +   ID +++K +  I  LKE + S I+ AVTG+I++
Sbjct: 396 GTKVILPDLLEQRNIAQYLDSKCKGIDSIIDKTKLQIDKLKEAKQSLISEAVTGKIEI 453


>gi|291540900|emb|CBL14011.1| Restriction endonuclease S subunits [Roseburia intestinalis XB6B4]
          Length = 445

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 117/241 (48%), Gaps = 19/241 (7%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE---SGKDIIYIGLEDVESG--TGKY 63
           Q K S + WIG +PK W V PIK       G  SE   S  +I   G+  + +G   G  
Sbjct: 4   QMKSSRIDWIGDVPKSWDVEPIKYRVSFYNGDRSENYPSKNEIQSEGIPFINAGHIEGNC 63

Query: 64  LPKDGNSRQSDTSTVSI----FAKGQILYGKLGPYLRKAIIADFD-GICSTQFLVLQPKD 118
           L  +     S+     +      +G ILY   G  + K II + D G  ++  + ++   
Sbjct: 64  LNMNDMDYISEEKYRVMGGVKLQQGDILYCLRGS-VGKNIIVNIDKGTVASSLVAIRSNG 122

Query: 119 VLPELLQGWLLS-IDVTQRIEAIC---EGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
           +L + L   L S ++  QR    C    G    +     +G   + IPP  EQ  I + +
Sbjct: 123 ILNKYLYYCLNSNVEEVQR----CLWDNGTAQPNLSADSLGKFKICIPPDHEQQAIADFL 178

Query: 175 IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
             E  +ID++  +  + I+LL++ K++L++  VTKGL+  V MKDSG+EW+G +P HW+ 
Sbjct: 179 DKECAQIDSIAADLEKQIDLLQQYKKSLITETVTKGLDKSVPMKDSGVEWIGKIPAHWDF 238

Query: 235 K 235
           K
Sbjct: 239 K 239



 Score = 63.2 bits (152), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 105/229 (45%), Gaps = 40/229 (17%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRK-------------------NTKLIESNI 256
           +MK S I+W+G VP  W+V+P    V+  N                     N   IE N 
Sbjct: 4   QMKSSRIDWIGDVPKSWDVEPIKYRVSFYNGDRSENYPSKNEIQSEGIPFINAGHIEGNC 63

Query: 257 LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV---MER 313
           L+++  + I + + R MG           +  G+I++         R      +   +++
Sbjct: 64  LNMNDMDYISEEKYRVMGGVK--------LQQGDILYCL-------RGSVGKNIIVNIDK 108

Query: 314 GIITSAYMAVKPHGIDSTYLAWLMRSY--DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPP 371
           G + S+ +A++ +GI + YL + + S   ++ +  +  G+  + +L  + + +  + +PP
Sbjct: 109 GTVASSLVAIRSNGILNKYLYYCLNSNVEEVQRCLWDNGTA-QPNLSADSLGKFKICIPP 167

Query: 372 IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
             EQ  I + ++ E A+ID +   +E+ I LL++ + S I   VT  +D
Sbjct: 168 DHEQQAIADFLDKECAQIDSIAADLEKQIDLLQQYKKSLITETVTKGLD 216



 Score = 44.7 bits (104), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 58/220 (26%), Positives = 98/220 (44%), Gaps = 24/220 (10%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKD--- 67
           KDSGV+WIG IP HW    +K F   N+  + + G     +   D  +  GK++      
Sbjct: 222 KDSGVEWIGKIPAHWDFKRLK-FMLENSSDSMKVGPFGSALSGSDF-TDEGKWVYNQRVV 279

Query: 68  -GNSRQSDTSTVS--------IFA--KGQILYGKLGPYLRKAIIAD--FDGI---CSTQF 111
             N+   +T+ VS         FA   G IL    G   + AI+ +   +GI   C  +F
Sbjct: 280 LDNNFSENTTFVSEEKFQEMRSFAVYPGDILITTRGTIGKVAIVPEGANEGILHPCIIKF 339

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWK-GIGNIPMPIPPLAEQVLI 170
            V   + ++PELLQ      D  +    +   AT     +   + +I +P+ P  EQ  I
Sbjct: 340 RV-DKEMIIPELLQLIFNESDFVKDQFTLMSNATTIEVIYSYSLKDILLPVIPADEQTKI 398

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALV-SYIVTK 209
              +  + + ID +I E+ + +  + + K++L+  Y+  K
Sbjct: 399 YGYLSKKCIVIDGIIAEKQKALATITQHKKSLIYEYVAGK 438


>gi|261212598|ref|ZP_05926882.1| type I restriction-modification system specificity subunit S
           [Vibrio sp. RC341]
 gi|260837663|gb|EEX64340.1| type I restriction-modification system specificity subunit S
           [Vibrio sp. RC341]
          Length = 248

 Score = 94.7 bits (234), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 121/246 (49%), Gaps = 30/246 (12%)

Query: 195 LKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNR-----KNT 249
           +KEK+QA++S+ VTKGLN +  MKDSG+EW+G VP+HW++K    +    N       + 
Sbjct: 1   MKEKRQAVISHAVTKGLNSNAPMKDSGVEWLGEVPEHWDMKRLKYIGEARNGLTYSPDDV 60

Query: 250 KLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQ 309
              E  IL L   NI    +   +      Y    I  P  I  +  DL    R+     
Sbjct: 61  VTQEEGILVLRSSNI----QDARLSFSDNVYVNMDI--PTRIRTKENDLLICSRNGSRQL 114

Query: 310 VMERGIIT--------SAYMAVKPHGIDSTYLAWLMRS--YDLCKVFYAMGSGLRQS--- 356
           + +  +IT         A+M V    I+  YL W++ S  +D     Y  GS L  +   
Sbjct: 115 IGKNALITKEAADMAFGAFMVVFRSKINP-YLYWVLNSPLFD-----YQSGSFLTSTINQ 168

Query: 357 LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           L   +++ + + +PP  EQ +I N +  ++   D L  K    + LLKER+++ I+AAVT
Sbjct: 169 LTIGNLENMEIPLPPECEQEEIKNYLIKKSDYFDDLTSKALHKVNLLKERKTALISAAVT 228

Query: 417 GQIDLR 422
           G+ID+R
Sbjct: 229 GKIDVR 234



 Score = 56.6 bits (135), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 52/222 (23%), Positives = 95/222 (42%), Gaps = 41/222 (18%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT--------SESG----------------K 46
           KDSGV+W+G +P+HW +  +K   +   G T         E G                 
Sbjct: 24  KDSGVEWLGEVPEHWDMKRLKYIGEARNGLTYSPDDVVTQEEGILVLRSSNIQDARLSFS 83

Query: 47  DIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGI 106
           D +Y+ ++         +P    ++++D    S     Q++ GK     ++A    F   
Sbjct: 84  DNVYVNMD---------IPTRIRTKENDLLICSRNGSRQLI-GKNALITKEAADMAFGA- 132

Query: 107 CSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
               F+V+    + P L   W+L+  +          +T++      + N+ +P+PP  E
Sbjct: 133 ----FMVVFRSKINPYLY--WVLNSPLFDYQSGSFLTSTINQLTIGNLENMEIPLPPECE 186

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           Q  I+  +I ++   D L ++ +  + LLKE+K AL+S  VT
Sbjct: 187 QEEIKNYLIKKSDYFDDLTSKALHKVNLLKERKTALISAAVT 228


>gi|147920296|ref|YP_685933.1| type I restriction modification system, specificity subunit
           [uncultured methanogenic archaeon RC-I]
 gi|110621329|emb|CAJ36607.1| type I restriction modification system, specificity subunit
           [uncultured methanogenic archaeon RC-I]
          Length = 484

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 62/161 (38%), Positives = 88/161 (54%), Gaps = 10/161 (6%)

Query: 46  KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG 105
           + I YIGLE +E  TGK L   GNS +  TST ++F KG +LYGKL PYL K  + + DG
Sbjct: 33  ESIPYIGLEHIEKDTGKLL-SFGNSTEV-TSTKTVFHKGDLLYGKLRPYLNKVCVTEIDG 90

Query: 106 ICSTQFLVLQPKDVLP-ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
           ICST  LV   +  L  +LL+  +L  D  +       G      D+K I +  + +PPL
Sbjct: 91  ICSTDILVFNEQRFLSNKLLKYRMLCPDFVRYANQNATGVNHPRVDFKKIASFEIALPPL 150

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSY 205
           AEQ     +I+A   +I+ L T+    +E LK+ K+ +  Y
Sbjct: 151 AEQ----HRIVA---KIEELFTQLDAGVEALKKAKEQIKQY 184


>gi|309390280|gb|ADO78160.1| restriction modification system DNA specificity domain protein
           [Halanaerobium praevalens DSM 2228]
          Length = 465

 Score = 94.0 bits (232), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 117/465 (25%), Positives = 212/465 (45%), Gaps = 52/465 (11%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY------IGLE 54
           M+ YK Y +Y+DSG++WI  IPK+W +  IK   K           D +Y      + ++
Sbjct: 2   MREYKRYEEYQDSGIEWIADIPKNWIISKIKYLVKEPVSDGPHETPDYVYDNGVPFLSVD 61

Query: 55  DVESGTGKYLPKDGNSRQSDTSTVSIF------AKGQILYGKLGPYLRKA-IIADFDGIC 107
            +++G   +     N RQ       I+       K  IL GK     + A I  DF    
Sbjct: 62  SIQNGKLVF----ENCRQISVKDHKIYRNKSNPEKEDILLGKAASVGKVAKINVDFPFSI 117

Query: 108 STQFLVLQPK-DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
            +   +++P   +    L+  + S     + + +    T  +   K I +I +  P + E
Sbjct: 118 WSPLALIKPNYKIESSYLEYSMKSSYFQIQTDLLSNSNTQKNLGMKDINDILVLKPSIEE 177

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKG------LNPD------ 214
           Q  I   +  +T  ID +  ++ + I+ L++ K+++++  VTKG      LN D      
Sbjct: 178 QQKIASFLDQKTAEIDEITNKKEKLIDQLEKYKKSVITDAVTKGKLGDKYLNEDGDLVDE 237

Query: 215 VKMKDSGIEWVGLVPDHWEVKPFFALVTELN-----RKNTK--LIESNILSLSYGNIIQK 267
           V+MKDSGIEW+  VP  +++      + +++     R  TK  L++    +L+ G   + 
Sbjct: 238 VEMKDSGIEWIRDVPHFYDISK-VKYIADIHGRIGYRGYTKDDLVDKGQGALTLGG--KH 294

Query: 268 LETRN-MGLKPESYETY-QIVDPGEIVFRFIDLQNDKR-SLRSAQVMERGI----ITSAY 320
           +  RN + L   +Y ++ +  +  EI+  + +L   +R S+    ++++ I    I  + 
Sbjct: 295 INDRNQLDLSDPTYISWDKYYESPEIMIEYNNLVVVQRGSIGKVAIIDKNIGEATINPSL 354

Query: 321 MAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSL-KFEDVKRLPVLVPPIKE--QFD 377
           + V    I + Y  + + S  + + F  + S     +   E +  L   +P I +  Q  
Sbjct: 355 ILVNNLEIKAKYFYYYLISNSVSEFFNLIVSSTAVPMISQEQLDNL--YLPKIDKHSQNK 412

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           I N ++ +T  ID L++K + SI   KE + S I  AVTG+IDLR
Sbjct: 413 IINYLDKKTELIDNLIQKTKTSIQKYKEYKKSLIFEAVTGKIDLR 457


>gi|293401124|ref|ZP_06645268.1| type I restriction-modification system specificity determinant
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305250|gb|EFE46495.1| type I restriction-modification system specificity determinant
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 464

 Score = 94.0 bits (232), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 106/446 (23%), Positives = 192/446 (43%), Gaps = 46/446 (10%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGL-------EDVESG 59
           Y +YK   + W+  IP HW V   K+          ++  + I + L        DV+SG
Sbjct: 4   YEEYKKIDLPWLNEIPAHWDVYRNKQIFTEMKDEVGKNSSNYILLSLTLNGVIPRDVKSG 63

Query: 60  TGKYLPKDGNSR--QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
            GK+       +  + D     +F         +    R   +A   G+ +  + +++  
Sbjct: 64  KGKFPASFDKYKIVEKDNLAFCLF--------DMDETPRTVGLAKCSGMLTGAYTIMKVS 115

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEG--ATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
           ++ P     + LS+D  + +  +  G   T++   + GI    MP+P   EQ  I   + 
Sbjct: 116 NINPRYAYYYYLSLDNVKGMRPLYTGLRKTINVGTFLGI---KMPVPTEEEQEQIVRFLD 172

Query: 176 AETVRIDTLITERIRFIELLKEKKQALV-SYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
            +  RI+++I  + + IELL+EK+Q ++ + ++T       +  + G  W   +P+ W++
Sbjct: 173 WQLSRINSIIKIKRKEIELLQEKRQQIIDAKVLTSSRTKVTRAAEGG--WNVNIPEGWDI 230

Query: 235 KPF---FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPES------YETYQI 285
             F   F+    LN     L E  I  +SYG +  K    N G K +        E+Y  
Sbjct: 231 LKFNGVFSFGKGLNITKANLEEEGIPVISYGQVHSK---NNPGTKIDDSLIRFVNESYLE 287

Query: 286 VDPGEIV----FRFIDLQNDKRSLRSAQVMER-GIITSAYMAV--KPH-GIDSTYLAWLM 337
             P  +V    F F D   D   + +   ++R G + + Y  V  +P  G  + YL++L 
Sbjct: 288 TSPNSLVYPGDFIFADTSEDFEGVGNCVFVDREGPLFAGYHTVIARPKDGNGNRYLSYLF 347

Query: 338 RSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKI 396
           +S           +G++  S+  + +K   V +PP+ EQ +I   ++     ID L+  I
Sbjct: 348 KSSTWRYQLRKNVNGVKVFSITQKVLKNAYVFLPPLDEQREIVEFLDEHCEGIDSLITDI 407

Query: 397 EQSIVLLKERRSSFIAAAVTGQIDLR 422
            + I LLK      I+   TG++D+R
Sbjct: 408 AKEIDLLKAYEMRLISDVSTGKVDVR 433


>gi|186685410|ref|YP_001868606.1| type I restriction enzyme, S subunit [Nostoc punctiforme PCC 73102]
 gi|186467862|gb|ACC83663.1| type I restriction enzyme, S subunit [Nostoc punctiforme PCC 73102]
          Length = 440

 Score = 94.0 bits (232), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 114/447 (25%), Positives = 188/447 (42%), Gaps = 52/447 (11%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y  YK   ++W+  IP+HWK+   K   +  +   S   +D I     D     G+   +
Sbjct: 6   YQAYKKCDIEWLLEIPEHWKIDRAKSLFREMSRPVSP--RDKIITVFRD-----GQVTLR 58

Query: 67  DGNSRQSDTSTVSIFA-----KGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--- 118
           +       T+ +  +      KG +++  +  +     ++D DG  + ++LV    D   
Sbjct: 59  ENRRVTGFTNAIEEYGYQGIRKGDLVFHAMDAFAGAIGVSDSDGKATPEYLVYTTIDKNK 118

Query: 119 --------VLPEL-LQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
                   +L ++ L G++L++  + R  +        H  +     + +PIPP  EQ  
Sbjct: 119 IYVPFFGFLLRQMALSGFVLALGKSVRERS----PRFKHTKFV---TLDLPIPPFTEQET 171

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVP 229
           I   +  +T +ID  I    +   L    KQ+L++  VT GL+  V M+DSGIEW+G VP
Sbjct: 172 IAHYLDTKTAQIDRKIDLLTQKATLYGNLKQSLINETVTCGLDKSVPMRDSGIEWIGEVP 231

Query: 230 DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQ--KLETRNMGLK-----PESYET 282
           +HW++K    L    N    K    + + +   N +   K E  N  L          E 
Sbjct: 232 EHWDIKRLKDLSDIQNSNVDKKSHDDEIPIKLCNYVDVYKNEFINTSLDFMDATANKSEI 291

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSAQVME--RGIITSAYMA---VKPHGIDSTYLAWLM 337
            Q       VF   D +        A   E  +G+I   ++A    K      +YL  L 
Sbjct: 292 KQFTIKEGDVFITKDSETCDDIAIPALAAESIKGVIYGYHLARLRTKEKVFLGSYLFRLF 351

Query: 338 --RSYDLCKVFYAMG---SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
             +SY    V  A G    GL QS   + +  +P+L     EQ  I + ++ +TA+ID +
Sbjct: 352 QSKSYGFRFVISAKGITRVGLGQSAIADSLTPVPLL----SEQKAIADYLDTKTAQIDQI 407

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQI 419
           ++ I   I  LKE R + I   VTG+I
Sbjct: 408 IQTINTQIEKLKELRKTLINDVVTGKI 434



 Score = 54.3 bits (129), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 93/211 (44%), Gaps = 14/211 (6%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKP 277
           K   IEW+  +P+HW++    +L  E++R  +   +  I     G +  +   R  G   
Sbjct: 10  KKCDIEWLLEIPEHWKIDRAKSLFREMSRPVSPR-DKIITVFRDGQVTLRENRRVTGFTN 68

Query: 278 --ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM---AVKPHGIDSTY 332
             E Y  YQ +  G++VF  +D       +  +     G  T  Y+    +  + I   +
Sbjct: 69  AIEEY-GYQGIRKGDLVFHAMDAFAGAIGVSDSD----GKATPEYLVYTTIDKNKIYVPF 123

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVK--RLPVLVPPIKEQFDITNVINVETARI 389
             +L+R   L     A+G  +R+ S +F+  K   L + +PP  EQ  I + ++ +TA+I
Sbjct: 124 FGFLLRQMALSGFVLALGKSVRERSPRFKHTKFVTLDLPIPPFTEQETIAHYLDTKTAQI 183

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           D  ++ + Q   L    + S I   VT  +D
Sbjct: 184 DRKIDLLTQKATLYGNLKQSLINETVTCGLD 214


>gi|149180787|ref|ZP_01859290.1| putative type I restriction enzyme specificity protein [Bacillus
           sp. SG-1]
 gi|148851577|gb|EDL65724.1| putative type I restriction enzyme specificity protein [Bacillus
           sp. SG-1]
          Length = 454

 Score = 93.2 bits (230), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 48/124 (38%), Positives = 76/124 (61%), Gaps = 1/124 (0%)

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEG-ATMSHADWKGIGNIPMPIPPLAEQVLI 170
           L  + KD+    L  +L S    + ++    G A  +    K I +  MP+P    Q  I
Sbjct: 125 LRCKSKDITNNFLFYFLNSHSYRKYLDLFAHGTANQASLSLKDILDFKMPLPSRKIQHQI 184

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
            E +  +T  ++TLI ++ + IELL+EK+QA+V+  VT+GLNPDVKMKDSG++W+G +P+
Sbjct: 185 SEFLDHKTSDVETLIADKQKLIELLEEKRQAIVTEAVTRGLNPDVKMKDSGVKWIGDIPE 244

Query: 231 HWEV 234
           HW++
Sbjct: 245 HWDI 248



 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 102/220 (46%), Gaps = 32/220 (14%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVES-GTGKYLP---- 65
           KDSGV+WIG IP+HW +  IK  T +  GR       I + GL   E    G YL     
Sbjct: 232 KDSGVKWIGDIPEHWDISKIKYSTYVK-GR-------IGWQGLRSDEFIDEGPYLVTGTD 283

Query: 66  -KDG-----------NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG--ICSTQF 111
            KDG             R S+   + +  +  +L  K G   + AI+ +  G  I ++  
Sbjct: 284 FKDGIIHWDTCYHISEERYSEAPPIQL-KENDLLITKDGTIGKVAIVKNKPGKAILNSGI 342

Query: 112 LV--LQPKDVLPELLQGWLLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
            V   Q K+ L + +  W+L+ +V +  I+ +  G+T+ H   +   N   P+P + EQ 
Sbjct: 343 FVTRCQDKEYLTKFMY-WILTSEVFKNYIKYMETGSTIKHLYQETFVNFSYPLPNIEEQK 401

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            I   +  +   ID++  E    IELLKE +Q+L+   VT
Sbjct: 402 AIEYFLETKVREIDSVKKEISDQIELLKEYRQSLIYEAVT 441



 Score = 42.7 bits (99), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
           + ++ W++ S         M +G   + L  E        +P I+EQ  I   +  +   
Sbjct: 354 TKFMYWILTSEVFKNYIKYMETGSTIKHLYQETFVNFSYPLPNIEEQKAIEYFLETKVRE 413

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           ID + ++I   I LLKE R S I  AVTG+IDLR
Sbjct: 414 IDSVKKEISDQIELLKEYRQSLIYEAVTGKIDLR 447



 Score = 42.7 bits (99), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 24/98 (24%), Positives = 51/98 (52%), Gaps = 2/98 (2%)

Query: 321 MAVKPHGIDSTYLAWLMRSYDLCKVF--YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDI 378
           +  K   I + +L + + S+   K    +A G+  + SL  +D+    + +P  K Q  I
Sbjct: 125 LRCKSKDITNNFLFYFLNSHSYRKYLDLFAHGTANQASLSLKDILDFKMPLPSRKIQHQI 184

Query: 379 TNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVT 416
           +  ++ +T+ ++ L+   ++ I LL+E+R + +  AVT
Sbjct: 185 SEFLDHKTSDVETLIADKQKLIELLEEKRQAIVTEAVT 222


>gi|167039866|ref|YP_001662851.1| restriction modification system DNA specificity subunit
           [Thermoanaerobacter sp. X514]
 gi|300915378|ref|ZP_07132692.1| restriction modification system DNA specificity domain protein
           [Thermoanaerobacter sp. X561]
 gi|307724809|ref|YP_003904560.1| restriction modification system DNA specificity domain-containing
           protein [Thermoanaerobacter sp. X513]
 gi|166854106|gb|ABY92515.1| restriction modification system DNA specificity domain
           [Thermoanaerobacter sp. X514]
 gi|300888654|gb|EFK83802.1| restriction modification system DNA specificity domain protein
           [Thermoanaerobacter sp. X561]
 gi|307581870|gb|ADN55269.1| restriction modification system DNA specificity domain protein
           [Thermoanaerobacter sp. X513]
          Length = 463

 Score = 92.8 bits (229), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 103/442 (23%), Positives = 182/442 (41%), Gaps = 40/442 (9%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           K YP+YK++   W+ +IP HW+   I+   +L   R SE   D  Y  L   ++G    +
Sbjct: 3   KPYPKYKETPALWLNSIPNHWESHKIR---ELFVER-SEKVSDKDYSPLSVSKAGVVPQI 58

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELL 124
                +   D   + I  KG  +          + I+++DG  S   +VL+P+  +    
Sbjct: 59  ATVAKTNNGDNRKLVI--KGDFVINSRSDRRGSSGISNYDGSVSLINIVLKPRSFVNGRY 116

Query: 125 QGWLLSIDVTQRIEAICEGATMSHAD-----WKGIGNIPMPIPPLAEQVLIREKIIAETV 179
             +LL       IE          AD     +  + +I +P+P + EQ  I   +  +  
Sbjct: 117 MHYLLKSHYF--IEEFYRNGRGIVADLWTTRYTEMKSIYLPVPSIEEQDQIVRFLDWKLA 174

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
           +I+ LI  + + I LL E ++A +  ++  G+NP    K+SG+ W+G +P HW V     
Sbjct: 175 KINKLIQAKKKQIALLTEYRKATIDNVIMYGINPHANRKESGVIWLGEIPSHWSVMK-LK 233

Query: 240 LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQ 299
            +  +N   T  +E    SL    +   +E  +   K +  E  ++ D       F   +
Sbjct: 234 RICRINASITSQLEK--YSLEDYVVFLPMENISSDGKIDCCEKRKLKDVRNGFSSF--AK 289

Query: 300 NDKRSLRSAQVMERG-------------------IITSAYMAVKPHGIDSTYLAWLMRSY 340
           ND    +     E G                   I+  A   V P  +   Y+   ++ +
Sbjct: 290 NDVIVAKITPCFENGKGACLDTLETNIGFGTTELIVLRANEKVLPRYL---YMITQLQQF 346

Query: 341 DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
            +       GS  ++ +    +    + +P I EQ +I   ++   A+ D L E + + I
Sbjct: 347 RIEGANVMTGSAGQKRVPSSFISNFELGIPSIAEQSEILEYLDNRLAKFDKLYETLNREI 406

Query: 401 VLLKERRSSFIAAAVTGQIDLR 422
            LL E R   I+  VTG++D+R
Sbjct: 407 ELLTEYRIRLISDVVTGKVDVR 428



 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/214 (24%), Positives = 107/214 (50%), Gaps = 12/214 (5%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLET 270
           L P  K K++   W+  +P+HWE      L  E + K +   + + LS+S   ++ ++ T
Sbjct: 2   LKPYPKYKETPALWLNSIPNHWESHKIRELFVERSEKVSDK-DYSPLSVSKAGVVPQIAT 60

Query: 271 RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-ID 329
                K  + +  ++V  G+ V   I+ ++D+R   S      G ++   + +KP   ++
Sbjct: 61  V---AKTNNGDNRKLVIKGDFV---INSRSDRRG-SSGISNYDGSVSLINIVLKPRSFVN 113

Query: 330 STYLAWLMRSYDLCKVFYAMGSGLRQSL---KFEDVKRLPVLVPPIKEQFDITNVINVET 386
             Y+ +L++S+   + FY  G G+   L   ++ ++K + + VP I+EQ  I   ++ + 
Sbjct: 114 GRYMHYLLKSHYFIEEFYRNGRGIVADLWTTRYTEMKSIYLPVPSIEEQDQIVRFLDWKL 173

Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           A+I+ L++  ++ I LL E R + I   +   I+
Sbjct: 174 AKINKLIQAKKKQIALLTEYRKATIDNVIMYGIN 207


>gi|225868036|ref|YP_002743984.1| type I restriction modification DNA specificity protein
           [Streptococcus equi subsp. zooepidemicus]
 gi|225701312|emb|CAW98328.1| type I restriction modification DNA specificity protein
           [Streptococcus equi subsp. zooepidemicus]
          Length = 415

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 117/230 (50%), Gaps = 13/230 (5%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRF-TKLNTGRTSESGKDIIYIGLEDV-----ESGTGKYL 64
           KDSG+ WIG +P +W+VVPIK F +K        +G++++ + +  V     E+ +GK +
Sbjct: 5   KDSGIDWIGEVPYNWRVVPIKSFLSKKKEILEKWTGENVLSLTMNGVVIRNLENPSGK-M 63

Query: 65  PKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELL 124
           P   +  Q       I     I    + P  R   IA  DG+ S  +   +  +   +  
Sbjct: 64  PTTFDGYQKIDKGSLILCLFDI---DVTP--RCVGIAYNDGVTSPAYSQYRIINGNLKFY 118

Query: 125 QGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
              LL +D  + +         +  D +  G + + IPPL+EQ  I + +  +   ID +
Sbjct: 119 YYLLLMMDNDKILLPYSRTLRSTLTD-EYFGAVKVVIPPLSEQEKIAQFLDKKIALIDDI 177

Query: 185 ITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
           +T+    IE LK  KQ+L++ IVTKGL+P VK+  SGIEWVG VP+ WEV
Sbjct: 178 VTDTKTSIEELKAYKQSLITEIVTKGLDPTVKLVSSGIEWVGNVPEGWEV 227



 Score = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 101/206 (49%), Gaps = 4/206 (1%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSY-GNIIQKLETRNMG 274
           KMKDSGI+W+G VP +W V P  + +++      K    N+LSL+  G +I+ LE  + G
Sbjct: 3   KMKDSGIDWIGEVPYNWRVVPIKSFLSKKKEILEKWTGENVLSLTMNGVVIRNLENPS-G 61

Query: 275 LKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLA 334
             P +++ YQ +D G ++    D+    R +  A     G+ + AY   +    +  +  
Sbjct: 62  KMPTTFDGYQKIDKGSLILCLFDIDVTPRCVGIA--YNDGVTSPAYSQYRIINGNLKFYY 119

Query: 335 WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           +L+   D  K+       LR +L  E    + V++PP+ EQ  I   ++ + A ID +V 
Sbjct: 120 YLLLMMDNDKILLPYSRTLRSTLTDEYFGAVKVVIPPLSEQEKIAQFLDKKIALIDDIVT 179

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQID 420
             + SI  LK  + S I   VT  +D
Sbjct: 180 DTKTSIEELKAYKQSLITEIVTKGLD 205



 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/198 (28%), Positives = 97/198 (48%), Gaps = 7/198 (3%)

Query: 13  SGVQWIGAIPKHWKVVPIKRFTKL-NTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSR 71
           SG++W+G +P+ W+VV IK  ++L N     E+G+   ++ LE + S    Y+       
Sbjct: 213 SGIEWVGNVPEGWEVVKIKNISQLRNEKDIYETGQK--FLALEKMLSYRPGYIDLLTEVE 270

Query: 72  QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSI 131
                 V I     +++ KL PYL K  I+DF+G  + + LV     +  +L    L+S 
Sbjct: 271 GGYQQVVKI---DDVVFSKLRPYLAKVAISDFEGFGTGELLVFHNIKINRKLFMYKLISE 327

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIP-PLAEQVLIREKIIAETVRIDTLITERIR 190
            + Q + +   G  M   +   I N+ +  P  L EQ +I + +  +T +IDTLI E+  
Sbjct: 328 QILQPVRSSSYGVKMPRVNPDFIMNLLISFPKSLYEQHIIADHLDQKTAQIDTLIVEKEN 387

Query: 191 FIELLKEKKQALVSYIVT 208
            I   +  K++++   VT
Sbjct: 388 LIREYETYKKSMIYEYVT 405


>gi|14520513|ref|NP_125988.1| type I restriction-modification enzyme, S subunit [Pyrococcus
           abyssi GE5]
 gi|5457728|emb|CAB49219.1| hsdS type I restriction-modification enzyme, S subunit [Pyrococcus
           abyssi GE5]
          Length = 427

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/192 (35%), Positives = 102/192 (53%), Gaps = 11/192 (5%)

Query: 21  IPKHWKVVPIKRFT-KLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           IP+ W VV +     + N      +  +I ++GLE +E G  + L + GNS     S+ S
Sbjct: 237 IPEEWDVVELGEVAERRNESVNPANMGNIPFVGLEHIEPGNIR-LSQWGNS-SEVKSSKS 294

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLLSIDVTQRI 137
            F  G ILYGKL PYL KA+IADF+GICST  +V++ K+   +PE L   + S +  +  
Sbjct: 295 KFYPGDILYGKLRPYLDKAVIADFEGICSTDIIVIKAKEDKTIPEYLIWVIHSKEFIEYA 354

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR-IDTLITERIRFIELLK 196
           +   +G       WK I    +P+PPL EQ     K IAE +R ID  I  +    E L+
Sbjct: 355 KKTMKGVNHPRTSWKSIKQFQIPLPPLEEQ-----KKIAEILRTIDEAIEAKRAKKEKLE 409

Query: 197 EKKQALVSYIVT 208
             K+A++  ++T
Sbjct: 410 RMKKAVMEKLLT 421



 Score = 45.1 bits (105), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 86/425 (20%), Positives = 178/425 (41%), Gaps = 46/425 (10%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           IP+ W+VV +    ++   ++     ++  I +E V      +   +  + + D  + + 
Sbjct: 26  IPEEWEVVELGEVARIRKKKSVRDIAEVAVIPMEKVPQDNELFAEFEIKAIE-DVKSSTY 84

Query: 81  FAKGQILYGKLGPYLR--KAIIADFD-----GICSTQFLVLQPKDVLPELLQGWLLSIDV 133
              G +L  K+ P     K  I  F+      + +T+   + P + L      ++L    
Sbjct: 85  CEAGDLLLAKITPSFENGKQGIVPFNVPNGFALATTEVYPIVPSENLDVFFLFYILKDKR 144

Query: 134 TQRI-EAICEGATMSHADWK-GIGNIPMPIPPLAEQVLIREKIIAETVR-IDTLITERIR 190
            ++I E    G T      K  +  + +P+PPL EQ     K IAE +R ID  I     
Sbjct: 145 FRKILEVRMTGTTGRQRVQKTDLLKLQIPLPPLEEQ-----KKIAEILRSIDEAIQAVDE 199

Query: 191 FIELLKEKKQALVSYIVTKGLN----PDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNR 246
            I  L+  K+  +  ++T+G+N      V++    +E    +P+ W+V     L     R
Sbjct: 200 SIARLERLKKGTMERLLTRGINHTRFKTVELNGRKVE----IPEEWDV---VELGEVAER 252

Query: 247 KNTKLIESNILSLSYGNIIQKLETRNM-----GLKPESYETYQIVDPGEIVFRFIDLQND 301
           +N  +  +N+ ++ +  + + +E  N+     G   E   +     PG+I++  +    D
Sbjct: 253 RNESVNPANMGNIPFVGL-EHIEPGNIRLSQWGNSSEVKSSKSKFYPGDILYGKLRPYLD 311

Query: 302 KRSLRSAQVMERGIITSAYMAVKPHGIDST---YLAWLMRSYDLCKVFYAMGSGLRQ-SL 357
           K  +   +    GI ++  + +K    D T   YL W++ S +  +       G+     
Sbjct: 312 KAVIADFE----GICSTDIIVIKAKE-DKTIPEYLIWVIHSKEFIEYAKKTMKGVNHPRT 366

Query: 358 KFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTG 417
            ++ +K+  + +PP++EQ  I  ++      ID  +E        L+  + + +   +TG
Sbjct: 367 SWKSIKQFQIPLPPLEEQKKIAEILRT----IDEAIEAKRAKKEKLERMKKAVMEKLLTG 422

Query: 418 QIDLR 422
           ++ +R
Sbjct: 423 EVRVR 427


>gi|66769483|ref|YP_244245.1| putative restriction endonuclease S subunits [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|188992673|ref|YP_001904683.1| Type I site-specific deoxyribonuclease (specificity subunit)
           [Xanthomonas campestris pv. campestris str. B100]
 gi|66574815|gb|AAY50225.1| putative restriction endonuclease S subunits [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|167734433|emb|CAP52643.1| Type I site-specific deoxyribonuclease (specificity subunit)
           [Xanthomonas campestris pv. campestris]
          Length = 438

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 97/372 (26%), Positives = 162/372 (43%), Gaps = 38/372 (10%)

Query: 79  SIFAKGQILYGKLGPYLR--KAIIAD--FDGIC--STQFLVLQPKDVLPELLQGWL-LSI 131
           + FA G +   K+ P     K  IA+   +G+   +T+  VL+P   L      +L ++ 
Sbjct: 69  TYFADGDVCIAKITPCFENGKGAIAEGLVNGVAFGTTELHVLRPSATLDTRFLFYLTIAH 128

Query: 132 DVTQRIEAICEGATMSH-------ADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
           D     EA   GA+           DW         +P +  Q  I   +  +T RID L
Sbjct: 129 DFRSHGEAEMLGASGQKRVPEEFLKDWTP------SLPRMDVQQRIARFLDDKTARIDAL 182

Query: 185 ITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTEL 244
           I ++   +E L+EK+QAL++  VTKGLNPD+ MK SG++W+G VP HWEVK     V  +
Sbjct: 183 IEKKQELLERLEEKRQALITRAVTKGLNPDLPMKPSGVDWLGYVPRHWEVKTLRRHVQRI 242

Query: 245 NRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETY--QIVDPG-EIVFRFIDLQND 301
            +  +   E  +       ++ K    N+G+  E+ +      +DP  E+  R  D+   
Sbjct: 243 EQGWSPQTERRMAEPDEWGVL-KSGCVNLGIYDENEQKALPGTLDPKPELEVRANDVLMC 301

Query: 302 KRS-----LRSAQVMERGIITSAY------MAVKPHGIDSTYLAWLMRSYDL---CKVFY 347
           + S     + S  ++ER      +      +++     D  Y   +M +  L    ++  
Sbjct: 302 RASGSMQYIGSVALVERTRTKLMFSDKTYRISLSSANTDREYFVRMMSAKHLREQIRLSV 361

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
           +   GL  ++   +V       PP+ EQ  I + +      +D    KI  S    +  R
Sbjct: 362 SGAEGLANNIPQSNVLEYLHAFPPLLEQVQIADFLRESIGDLDEAEGKIRASSESWRAYR 421

Query: 408 SSFIAAAVTGQI 419
            + + AAVTGQ+
Sbjct: 422 LALVTAAVTGQL 433



 Score = 39.7 bits (91), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 35/142 (24%), Positives = 67/142 (47%), Gaps = 5/142 (3%)

Query: 280 YETYQIVDPGEIVFRFID--LQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWL 336
           Y  Y     G++    I    +N K ++    V      T+    ++P   +D+ +L +L
Sbjct: 65  YNGYTYFADGDVCIAKITPCFENGKGAIAEGLVNGVAFGTTELHVLRPSATLDTRFLFYL 124

Query: 337 MRSYDLCKVFYA--MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
             ++D      A  +G+  ++ +  E +K     +P +  Q  I   ++ +TARID L+E
Sbjct: 125 TIAHDFRSHGEAEMLGASGQKRVPEEFLKDWTPSLPRMDVQQRIARFLDDKTARIDALIE 184

Query: 395 KIEQSIVLLKERRSSFIAAAVT 416
           K ++ +  L+E+R + I  AVT
Sbjct: 185 KKQELLERLEEKRQALITRAVT 206


>gi|323351172|ref|ZP_08086828.1| hypothetical protein HMPREF9398_0876 [Streptococcus sanguinis
           VMC66]
 gi|322122396|gb|EFX94107.1| hypothetical protein HMPREF9398_0876 [Streptococcus sanguinis
           VMC66]
          Length = 433

 Score = 91.3 bits (225), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 106/435 (24%), Positives = 193/435 (44%), Gaps = 36/435 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVES-GTGKYLP---- 65
           K+SG+ WIG IP+ W+V+ +K FT +  GR       I + GL+  E    G YL     
Sbjct: 5   KESGIDWIGQIPEEWEVIKVKFFTYMK-GR-------IGWQGLKADEFIDEGPYLVTGTD 56

Query: 66  -KDGNSRQSDTSTVSI----------FAKGQILYGKLGPYLRKAIIADFDGICS--TQFL 112
            K+G         +S             +G +L  K G   + A+I +     S  +  L
Sbjct: 57  FKNGRVNWDTAYHISQKRYEQAPEIQLKQGDLLVTKDGTVGKLALIDELPDSASLNSHLL 116

Query: 113 VLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           VL+P         L   L S++     + +  G+TM     + +G     +P + EQ  I
Sbjct: 117 VLRPLFNRYENHFLYYVLSSLEFKNYFQKVSIGSTMDSLSQEKMGEFIFALPNINEQNSI 176

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              +  +T ++D + +     I+ LK+ + +L+   VTKGL+  V +KDSGI+W+G VP+
Sbjct: 177 SRYLDKKTAQLDKVKSLLEEQIQKLKDYRSSLIYETVTKGLDKTVPLKDSGIDWIGHVPE 236

Query: 231 HWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQ-----KLETRNMGLKPESYETYQI 285
            W VK    +  E+   +T   ++ I      N IQ     + +T     K  SY+ ++ 
Sbjct: 237 GWGVKAIKYIFDEIGSGSTPKSDNEIFYDGDINWIQSGDLYQTDTVTSVSKTISYQGFKS 296

Query: 286 VDPGEIVFR-FIDLQNDKRSLRSAQVME-RGIITSAYMAVKPHGIDSTYLAWLMRSYDLC 343
               +I  + F+ L     S+ +  V      +  A +A+       ++  + + +    
Sbjct: 297 TSALKIYQQPFVALAMYGASVGNVAVSYIDACVNQAVVAMLGSSEKVSFGKYAIEASKSN 356

Query: 344 KVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
            +F A G G + ++    +K   +  P  +EQ  + + ++ +T +ID L++   + I  +
Sbjct: 357 LIFSAQG-GTQPNISQNLIKNWSIPQPKNEEQEQVVDFLDKKTVQIDKLIQIKNEQIKNI 415

Query: 404 KERRSSFIAAAVTGQ 418
            ++R + I   VTG+
Sbjct: 416 NKQRQTLIYDYVTGK 430



 Score = 47.4 bits (111), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 95/231 (41%), Gaps = 39/231 (16%)

Query: 215 VKMKDSGIEWVGLVPDHWEV--KPFFA----------------------LVTELNRKNTK 250
            +MK+SGI+W+G +P+ WEV    FF                       LVT  + KN +
Sbjct: 2   TRMKESGIDWIGQIPEEWEVIKVKFFTYMKGRIGWQGLKADEFIDEGPYLVTGTDFKNGR 61

Query: 251 LIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV 310
           +       +S     Q  E +   LK       +    G++    ID   D  SL S  +
Sbjct: 62  VNWDTAYHISQKRYEQAPEIQ---LKQGDLLVTKDGTVGKLAL--IDELPDSASLNSHLL 116

Query: 311 MERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSG-LRQSLKFEDVKRLPVLV 369
           + R +             ++ +L +++ S +    F  +  G    SL  E +      +
Sbjct: 117 VLRPLFNR---------YENHFLYYVLSSLEFKNYFQKVSIGSTMDSLSQEKMGEFIFAL 167

Query: 370 PPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           P I EQ  I+  ++ +TA++D +   +E+ I  LK+ RSS I   VT  +D
Sbjct: 168 PNINEQNSISRYLDKKTAQLDKVKSLLEEQIQKLKDYRSSLIYETVTKGLD 218


>gi|148656808|ref|YP_001277013.1| restriction modification system DNA specificity subunit
           [Roseiflexus sp. RS-1]
 gi|148568918|gb|ABQ91063.1| restriction modification system DNA specificity domain [Roseiflexus
           sp. RS-1]
          Length = 290

 Score = 89.7 bits (221), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 61/183 (33%), Positives = 88/183 (48%), Gaps = 8/183 (4%)

Query: 18  IGAIPKHWKVVPIKRFTKLNT-GRTSESGKDIIYIGLEDVESGTGK--YLPKDGNSRQSD 74
           IG +P HW+VV +     L T G    +     YIGLE +E G  +  +  K  + R   
Sbjct: 75  IGPLPAHWRVVRLGEVATLFTRGIDPANAGAKRYIGLEHIEPGNIRIQHWGKADDVRSLK 134

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELLQGWLLSIDV 133
           T+    F +G +LYGKL PYL KA++A++DGICST  LV++ +  +LPE L   + +   
Sbjct: 135 TA----FQQGDVLYGKLRPYLDKAVLAEWDGICSTDILVIKAQSSLLPEFLAYLVHTSQF 190

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIE 193
                +   G       WK +   P+ +PPL EQ  I   + A   +I      R    E
Sbjct: 191 IDYAISTTTGVNHPRTSWKALQKFPISLPPLDEQREIARMLQAVDAKIAAEQARRAALEE 250

Query: 194 LLK 196
           L K
Sbjct: 251 LFK 253


>gi|262196003|ref|YP_003267212.1| restriction modification system DNA specificity domain protein
           [Haliangium ochraceum DSM 14365]
 gi|262079350|gb|ACY15319.1| restriction modification system DNA specificity domain protein
           [Haliangium ochraceum DSM 14365]
          Length = 423

 Score = 89.7 bits (221), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 107/425 (25%), Positives = 187/425 (44%), Gaps = 44/425 (10%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIY-----IGLEDVESGTGKYLPKDGNSRQSDT 75
           +P  W+ V +     L +G+     +D  Y     +    +ES TG+ L  +    Q+  
Sbjct: 7   VPTRWRRVRLLDHVDLPSGQVDP--RDPQYRSQPLVAPNHIESQTGRLLALESAESQNAI 64

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELLQGWLLSIDVT 134
           S    F+ G ++Y K+ PYLRKAI+A FDG+CS     L+ K  V P  L   LL  + +
Sbjct: 65  SGKYTFSAGDVVYSKIRPYLRKAILASFDGLCSADMYPLRAKTSVEPGFLLALLLGEEFS 124

Query: 135 QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIEL 194
              E++     +   + K +G+    +PPL EQ     KI A    +D  I      IE 
Sbjct: 125 SFAESVSMRTGIPKLNRKELGSYHARLPPLGEQ----RKIAAILGAVDEAIARTQAVIEQ 180

Query: 195 LKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV--------------KPFFAL 240
           ++  K+ L+  ++T+GL P    +    E +G +P+ W                 P  A 
Sbjct: 181 VQVVKKGLMQDLLTRGL-PGRHTRFKQTE-IGQIPESWSAVRLGDVLDGIDAGWSPKCAN 238

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
               N +   L  S++ S  Y     K+   ++  KPE       V PG+++        
Sbjct: 239 HPAGNGEWGVLKVSSVSSGIYKPEENKMLPDDLIPKPELE-----VRPGDVIIARASGVL 293

Query: 301 DKRSLRS--AQVMERGIITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVFY--AMGSGLR 354
           D   + S   +   R +++   + V+P+   +DS YLA  ++S  +  +    A GS +R
Sbjct: 294 DLVGVCSFVYKTRPRLMLSDKTLRVRPNRTLLDSFYLALTLQSPVVRSLVLEKATGSHMR 353

Query: 355 QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAA 414
            ++  + +  + V +P + EQ  +++ I    ARID     +E     L E +S+ ++  
Sbjct: 354 -NISQKAIGSVTVALPSLDEQVKVSSGIMAMDARIDNDTRSVES----LTELKSALMSVL 408

Query: 415 VTGQI 419
           +TG++
Sbjct: 409 LTGEV 413


>gi|227500130|ref|ZP_03930201.1| restriction endonuclease S subunits [Anaerococcus tetradius ATCC
           35098]
 gi|227217772|gb|EEI83072.1| restriction endonuclease S subunits [Anaerococcus tetradius ATCC
           35098]
          Length = 424

 Score = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 120/444 (27%), Positives = 193/444 (43%), Gaps = 70/444 (15%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESG----TGKYLPK 66
           KDSG+ WIG +P  WKV  IK   +LN GR    G        E ++ G    TG    K
Sbjct: 5   KDSGINWIGTMPNDWKVKKIKYIGELN-GRIGWQG----LTSNEYIDEGPFLITGTDF-K 58

Query: 67  DG-----------NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           DG           +SR  +   + I   G +L  K G   + AI+ + +G+ S    VL+
Sbjct: 59  DGRIDWDTCVHIDHSRWEEAKKIQI-KNGDLLITKDGTVGKVAIVENLEGLASLNSGVLK 117

Query: 116 ---PKDVLPELLQGWLLSIDV--TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
               +  L + L  ++L  DV  T         +T+ H   K   N    IP   EQ +I
Sbjct: 118 IDLKEGYLAKFLF-YVLQSDVFWTWFNYTSSGNSTILHLYEKDFNNFTFSIPDKDEQEVI 176

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
              + +    I+  I++  + I++LKE  ++LVS  +TKGL  +V+ KD+ I+W+G +P 
Sbjct: 177 INFLDSNVGSINLKISKIEKQIKILKEYIKSLVSETITKGLEKNVEYKDTSIDWIGKIPA 236

Query: 231 HWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD 287
           +W +   K  F +    +   +   E+        N IQK    +  L+ +    Y    
Sbjct: 237 NWSIKRLKHLFYIYAGGDIDYSDYAEAE-------NEIQKYPILSNSLEHDGVIGYT--- 286

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVMERGIITSA-------YMAVK-----PHGIDST-YLA 334
                FRF   + D     +  V  RG++  A       Y  V+     P   D   Y +
Sbjct: 287 ---SKFRF---EGD-----TITVTGRGLVGVAVPRNFKFYPVVRLLVGEPKDRDDVRYFS 335

Query: 335 WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           + + S ++     AM    R+  K  D+K   V  P  K Q +I N ++ E ++I+ ++E
Sbjct: 336 YCINSANVIGDQTAMAQLTRE--KLGDIK---VPYPLKKIQIEIANFLDTEVSKINHVIE 390

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQ 418
             EQ I  L + ++S +   VTG+
Sbjct: 391 TKEQQITKLIDYKNSLVYEYVTGK 414



 Score = 40.0 bits (92), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 48/212 (22%), Positives = 86/212 (40%), Gaps = 33/212 (15%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDG 68
           +YKD+ + WIG IP +W +  +K    +       +G DI Y    + E+   KY P   
Sbjct: 222 EYKDTSIDWIGKIPANWSIKRLKHLFYI------YAGGDIDYSDYAEAENEIQKY-PILS 274

Query: 69  NSRQSD------------TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
           NS + D              T+++  +G +           A+  +F      + LV +P
Sbjct: 275 NSLEHDGVIGYTSKFRFEGDTITVTGRGLV---------GVAVPRNFKFYPVVRLLVGEP 325

Query: 117 KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
           KD        + ++         I +   M+    + +G+I +P P    Q+ I   +  
Sbjct: 326 KDRDDVRYFSYCIN-----SANVIGDQTAMAQLTREKLGDIKVPYPLKKIQIEIANFLDT 380

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           E  +I+ +I  + + I  L + K +LV   VT
Sbjct: 381 EVSKINHVIETKEQQITKLIDYKNSLVYEYVT 412


>gi|189499314|ref|YP_001958784.1| restriction modification system DNA specificity domain [Chlorobium
           phaeobacteroides BS1]
 gi|189494755|gb|ACE03303.1| restriction modification system DNA specificity domain [Chlorobium
           phaeobacteroides BS1]
          Length = 430

 Score = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 61/192 (31%), Positives = 94/192 (48%), Gaps = 13/192 (6%)

Query: 45  GKDIIYIGLEDVESGTGKYLPKDGNSRQSDT-STVSIFAKGQILYGKLGPYLRKAIIADF 103
           G +  YIGLE +  G   ++   G  ++ +  S+ ++F  G IL+GKL PYLRK   ADF
Sbjct: 70  GGEKPYIGLEHLAQGFPAFI---GRGKECEVKSSKTVFKSGDILFGKLRPYLRKGAQADF 126

Query: 104 DGICSTQFLVLQPKDVL-PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
           DGICST  LV + K +     L+  + S +     +    G       W  +    + +P
Sbjct: 127 DGICSTDILVFRAKPICESNFLRFVIHSEEFVAHAKTTTSGVRHPRTSWPLLREFYISLP 186

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
           PL EQ    +KI      +   I  + R I+   E K+AL+  + T+GL  + + +    
Sbjct: 187 PLPEQ----KKIAHILSTVQRAIEAQDRIIQTTTELKKALMHKLFTEGLRNEPQKEAE-- 240

Query: 223 EWVGLVPDHWEV 234
             +GLVP+ WEV
Sbjct: 241 --IGLVPESWEV 250


>gi|257440746|ref|ZP_05616501.1| type I restriction-modification [Faecalibacterium prausnitzii
           A2-165]
 gi|257196807|gb|EEU95091.1| type I restriction-modification [Faecalibacterium prausnitzii
           A2-165]
          Length = 275

 Score = 87.4 bits (215), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 72/287 (25%), Positives = 132/287 (45%), Gaps = 44/287 (15%)

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           + +PP   Q+   + + A+   IDT++++    IE  K+ KQA+++  VTKG+  + +MK
Sbjct: 3   LALPPKEIQIRSAQYLNAKCTEIDTMLSKTRSSIEEYKKLKQAVITQAVTKGVRGEREMK 62

Query: 219 DSGIEWVGLVPDHWEVKPFFAL------VTELNRKNTKLIES------NILSLSYGNIIQ 266
           D G+EW GLVP HW V    ++       T L  K +   +         L L+ G +  
Sbjct: 63  DCGVEWAGLVPHHWGVAKIGSIGQTSSGATPLRSKESSFFDDATIRWVRTLDLNDGFVYD 122

Query: 267 K--------LETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQ--VMERGII 316
                    L +    + P+      +      + +   L +D  + ++    V  R I+
Sbjct: 123 SSEKITELALASSACSIMPKGTVCVAMYGGAGTIGKCGLLMSDCATNQAVCSIVCNRKIV 182

Query: 317 TSAY-----MAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPP 371
           +  +     +A+KP+        W+          YA+G+    ++  + V R+ +L+PP
Sbjct: 183 SPIFLLMQLLALKPY--------WMK---------YAVGTRKDPNISQDIVARMKILIPP 225

Query: 372 IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           + EQ +IT+ ++ + A ID L+ K EQ +  L+  + S I   VTG+
Sbjct: 226 LDEQKEITDYLDAKCAEIDKLIAKKEQLVKELESYKKSLIYEVVTGK 272



 Score = 49.7 bits (117), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 97/221 (43%), Gaps = 31/221 (14%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD--------IIYIGLEDVESGT 60
           + KD GV+W G +P HW V  I    + ++G T    K+        I ++   D+  G 
Sbjct: 60  EMKDCGVEWAGLVPHHWGVAKIGSIGQTSSGATPLRSKESSFFDDATIRWVRTLDLNDG- 118

Query: 61  GKYLPKDGNSRQSD----TSTVSIFAKGQI---LYGKLGPYLRKAII----ADFDGICST 109
                 D + + ++    +S  SI  KG +   +YG  G   +  ++    A    +CS 
Sbjct: 119 ---FVYDSSEKITELALASSACSIMPKGTVCVAMYGGAGTIGKCGLLMSDCATNQAVCS- 174

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKG--IGNIPMPIPPLAEQ 167
             +V   K V P  L   LL++       A+    T    +     +  + + IPPL EQ
Sbjct: 175 --IVCNRKIVSPIFLLMQLLALKPYWMKYAV---GTRKDPNISQDIVARMKILIPPLDEQ 229

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             I + + A+   ID LI ++ + ++ L+  K++L+  +VT
Sbjct: 230 KEITDYLDAKCAEIDKLIAKKEQLVKELESYKKSLIYEVVT 270


>gi|33240157|ref|NP_875099.1| restriction endonuclease S subunit [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33237684|gb|AAP99751.1| Restriction endonuclease S subunit [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
          Length = 425

 Score = 87.0 bits (214), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 86/360 (23%), Positives = 164/360 (45%), Gaps = 26/360 (7%)

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDV 133
           +  ++ I+ +  I+    G  + +  I  F    +    VL P +   EL   +   I +
Sbjct: 79  NNPSLKIYPRNSIIIAMYGATIGRVSIPKFSFTVNQACCVLSPFNKC-ELKYLFYCLIGL 137

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIE 193
              + ++  G    + + + I ++ + +P   EQ  I + +  E ++I+  I  +   I 
Sbjct: 138 RHVLFSMAIGGAQPNINQELIKSLKILLPSNYEQKKIYKFLDQEIIKINLAIQNQYNLIT 197

Query: 194 LLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIE 253
           LL EKKQALV   +TKGL+ +V MK+S +  +G +P+HW+ K    L      KN++ + 
Sbjct: 198 LLDEKKQALVLDAITKGLDKEVSMKNSKLFLLGKIPNHWQSKKLSQLFKTSKGKNSQKLT 257

Query: 254 SNILSLSYGNI-IQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME 312
               S + G+  +   +T++ G+   +Y      D GE   + + L     +   A+ M 
Sbjct: 258 KEYCSKNEGDYPVYSGQTQSDGIM--AYINTFEFDAGE---KGVIL----TTTVGAKAMS 308

Query: 313 RGIITSAY--------MAVKPHGIDSTYLAWLMRS---YDLCKVFYAMGSGLRQSLKFED 361
             +I   +        ++ K +   + Y  +   S    +  K+   M    R+    ED
Sbjct: 309 VKLIKGRFNLSQNCMVISAKDNSCHTAYFEYCFSSIFKIEKNKIPIHMQPSFRK----ED 364

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            +++ + +PPIKEQ  I+N ++ E  +I  + E  +  I  L ++R + I+ A + QIDL
Sbjct: 365 FQKIRIPIPPIKEQIQISNFLHKEVEKIKQMNESSKLLISKLIDKRFALISFATSNQIDL 424


>gi|28199931|ref|NP_780245.1| type I restriction-modification system specificity determinant
           [Xylella fastidiosa Temecula1]
 gi|182682685|ref|YP_001830845.1| restriction modification system DNA specificity subunit [Xylella
           fastidiosa M23]
 gi|28058062|gb|AAO29894.1| type I restriction-modification system specificity determinant
           [Xylella fastidiosa Temecula1]
 gi|182632795|gb|ACB93571.1| restriction modification system DNA specificity domain [Xylella
           fastidiosa M23]
 gi|307578969|gb|ADN62938.1| restriction modification system DNA specificity subunit [Xylella
           fastidiosa subsp. fastidiosa GB514]
          Length = 444

 Score = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 101/440 (22%), Positives = 171/440 (38%), Gaps = 59/440 (13%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG-LEDVESGTGKYLP 65
           YP Y+   ++W+ A+P+HW     K F +    R+    ++++ +  L  V S + K + 
Sbjct: 7   YPNYRQPKMRWLPAVPEHWNEQRAKTFFREVDERSKTGQEELLSVSHLTGVTSRSQKNVT 66

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV------ 119
                + +      +   G I+   L  ++     +   GI S  + V +P         
Sbjct: 67  M---FKAASYVGSKLCRPGDIVINTLWAWMAALGASRHVGIVSPAYGVYRPHHADSFNPA 123

Query: 120 -LPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
            L  LL+      +   R   I       + +     +I +  PP  EQ  I   + A+ 
Sbjct: 124 YLDYLLRTRAYVAEYIGRSTGIRSSRLRLYPN--QFLDIALIQPPRPEQDQIVAYLRAQD 181

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF- 237
             I   I  +   I+LL E+K  ++ + VT+GL+  V +K SGIEW+G VP H  ++   
Sbjct: 182 AHIARFIKAKRDLIKLLTEQKLRIIDHAVTRGLDASVALKPSGIEWLGDVPVHCRIERLK 241

Query: 238 ----FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVF 293
               F     L+  N +           GN+        +G+    ++   +V P  ++ 
Sbjct: 242 WVCRFTYGDSLSDANRR----------QGNVPVYGSNGPVGM----HDVANVVGPCIVIG 287

Query: 294 RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLA----------WLMRSYDLC 343
           R       K S       E  +            ID+TY            WL      C
Sbjct: 288 R-------KGSFGKVNYSESDLF----------AIDTTYFVDKKCTKANIRWLYYVLIWC 330

Query: 344 KVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
           ++           L   D     V VP   EQ  I   +++ETA ++  + K+E+ I L+
Sbjct: 331 RLDRISKDSAVPGLDRTDALNTLVPVPDGAEQEQIAKQLDIETAEVNDAITKVEEEITLI 390

Query: 404 KERRSSFIAAAVTGQIDLRG 423
           +E R   I   VTGQ+D+RG
Sbjct: 391 REYRDRLITDVVTGQVDVRG 410



 Score = 46.6 bits (109), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 49/212 (23%), Positives = 94/212 (44%), Gaps = 22/212 (10%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS 70
           K SG++W+G +P H ++  +K   +   G +           L D     G  +P  G++
Sbjct: 221 KPSGIEWLGDVPVHCRIERLKWVCRFTYGDS-----------LSDANRRQGN-VPVYGSN 268

Query: 71  RQSDTSTVSIFAKGQILYGKLGPYLR-KAIIADFDGICSTQFLVLQPKDVLPELLQGWLL 129
                  V+      I+ G+ G + +     +D   I +T F+    K      ++ WL 
Sbjct: 269 GPVGMHDVANVVGPCIVIGRKGSFGKVNYSESDLFAIDTTYFV---DKKCTKANIR-WLY 324

Query: 130 SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERI 189
            + +  R++ I + + +   D     N  +P+P  AEQ  I +++  ET  ++  IT+  
Sbjct: 325 YVLIWCRLDRISKDSAVPGLDRTDALNTLVPVPDGAEQEQIAKQLDIETAEVNDAITKVE 384

Query: 190 RFIELLKEKKQALVSYIVT-----KGLNPDVK 216
             I L++E +  L++ +VT     +G  PDV+
Sbjct: 385 EEITLIREYRDRLITDVVTGQVDVRGWQPDVE 416


>gi|220931290|ref|YP_002508198.1| restriction modification system DNA specificity domain protein
           [Halothermothrix orenii H 168]
 gi|219992600|gb|ACL69203.1| restriction modification system DNA specificity domain protein
           [Halothermothrix orenii H 168]
          Length = 422

 Score = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/190 (33%), Positives = 94/190 (49%), Gaps = 10/190 (5%)

Query: 21  IPKHWKVVPIKR-FTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           IP  W ++     F K N     E  K+  Y+GLE + +G    L  D N   ++ S+  
Sbjct: 229 IPVVWTLIKFGEVFKKRNEKANVE--KEYKYVGLEHLGTGEINLLGYDRNG--NNKSSKR 284

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFL-VLQPKDVLPELLQGWLLSIDVTQRIE 138
           +F  G ILYGKL PYL+KA I DFDGICST  + +   K  +   L   + S        
Sbjct: 285 LFKSGDILYGKLRPYLKKAAITDFDGICSTDIIPIYATKKSVNNYLIYLVHSKMFVDFAV 344

Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK 198
           +  EG  +    W+ I N+ +P+PPL EQ    +KI +    +D  I +   + E L+E 
Sbjct: 345 STMEGTNLPRTSWRVIKNLIIPLPPLQEQ----KKIASILSSVDEKIQKEQEYREKLEEL 400

Query: 199 KQALVSYIVT 208
           K+ L+  ++T
Sbjct: 401 KKGLMQKLLT 410



 Score = 40.8 bits (94), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 95/445 (21%), Positives = 184/445 (41%), Gaps = 81/445 (18%)

Query: 21  IPKHWKVVPIKRFTK-LNTGRTSES------GKDIIYIGLEDVESGTGKYLPKDGNSRQS 73
           IPK W+       +K +  G T ++      G +I+++ +ED+ +  GKY+    ++   
Sbjct: 18  IPKEWEFRNFGLISKYIKAGGTPKADKKEYYGGEILFVKIEDM-TKNGKYIYNTKSTITE 76

Query: 74  D---TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLS 130
           D    S+  I  K  +L    G Y  K  I   +   +   L + P + +  L   +  S
Sbjct: 77  DGLKNSSAWIVPKKSLLLSMYGSY-GKVSINKVELATNQAILGIIPSEEV-NLDYLYYFS 134

Query: 131 IDVTQ-RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERI 189
           +   +   +++ +  T ++   + + N P+  PPL EQ    +KI A    +D  I +  
Sbjct: 135 LGCLKPYFKSLVKATTQANLTKQIVNNTPVLSPPLPEQ----KKIAAILSTVDKAIEKTD 190

Query: 190 RFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT 249
             IE  KE K+ L+  ++TKG+                   H E K          R  T
Sbjct: 191 EIIEKSKELKKGLMQQLLTKGIG------------------HSEFKEV--------RIGT 224

Query: 250 KLIESNIL--SLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRS 307
           K I+  ++   + +G + +K   +    K   Y   + +  GEI     D   + +S  S
Sbjct: 225 KKIKIPVVWTLIKFGEVFKKRNEKANVEKEYKYVGLEHLGTGEINLLGYDRNGNNKS--S 282

Query: 308 AQVMERGIITSAYMAVKPH----------GIDST--------------YLAWLMRSYDLC 343
            ++ + G I   Y  ++P+          GI ST              YL +L+ S    
Sbjct: 283 KRLFKSGDI--LYGKLRPYLKKAAITDFDGICSTDIIPIYATKKSVNNYLIYLVHSKMFV 340

Query: 344 --KVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
              V    G+ L ++  +  +K L + +PP++EQ  I +++    + +D  ++K ++   
Sbjct: 341 DFAVSTMEGTNLPRT-SWRVIKNLIIPLPPLQEQKKIASIL----SSVDEKIQKEQEYRE 395

Query: 402 LLKERRSSFIAAAVTGQIDLRGESQ 426
            L+E +   +   +TG++ ++ E +
Sbjct: 396 KLEELKKGLMQKLLTGEVRVKVEDE 420


>gi|152998552|ref|YP_001355473.1| restriction modification system DNA specificity subunit [Shewanella
           baltica OS185]
 gi|151367566|gb|ABS10565.1| restriction modification system DNA specificity domain [Shewanella
           baltica OS185]
          Length = 388

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 109/436 (25%), Positives = 179/436 (41%), Gaps = 62/436 (14%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           M HYK Y +YK + + W+ ++P HWK+   KR   +N G   +            +ES  
Sbjct: 1   MSHYKPYLEYKGTDLAWLKSVPSHWKIAQFKRLISINNGSDHKQ-----------IESDD 49

Query: 61  GKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP---K 117
           G  +   G         V  +AK  I  G+     RK  I D       +F  +      
Sbjct: 50  GYPVYGSGG--------VFAYAKDYIHDGESVLLGRKGTI-DKPLYVKGKFWTVDTMYWS 100

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
            +LP     +   I  T           +       +G+  +  P   EQ  I   +  E
Sbjct: 101 KILPTANGKFCYYIATTIPFGLYSTNTALPSMTQTDLGSHVVAFPDYNEQTEITRVLDCE 160

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF 237
           T RID LI ++ RF+EL+KEK  ALV      G     ++K                   
Sbjct: 161 TTRIDALIRKKSRFLELIKEKILALVMNEQINGNGKFDRLK------------------- 201

Query: 238 FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPGEIVFRFI 296
             +   ++R  T +     ++L   N  + L  + + L K     ++  V+ G+++    
Sbjct: 202 -RMTNVVSRPATIVDSDEYVALGLYNRGRGLFHKPVTLGKDMGDSSFFYVEEGDLIL--- 257

Query: 297 DLQNDKRSLRSAQVM----ERGIITSA-YMAVKPHGIDSTYL-AWLMRSYD--LCKVFYA 348
              + + +   A  M    E G + S  Y  ++   I + YL A  M ++   L      
Sbjct: 258 ---SGQFAWEGAVTMATEKETGCVVSHRYPVIRGKSIATEYLFALFMTNFGDFLLNESSR 314

Query: 349 MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRS 408
             +G  + L    +    + +P  + Q ++  ++ ++ A+ DV   K+++SI LLKERRS
Sbjct: 315 GAAGRNRPLNINLLLNEKIRIPSPEVQREVKRLMYLK-AQADV---KVKKSIALLKERRS 370

Query: 409 SFIAAAVTGQIDLRGE 424
           +FI AAVTG+IDLRGE
Sbjct: 371 AFITAAVTGKIDLRGE 386


>gi|313892700|ref|ZP_07826281.1| conserved hypothetical protein [Veillonella sp. oral taxon 158 str.
           F0412]
 gi|313442631|gb|EFR61042.1| conserved hypothetical protein [Veillonella sp. oral taxon 158 str.
           F0412]
          Length = 470

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 101/456 (22%), Positives = 185/456 (40%), Gaps = 57/456 (12%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYI-----GLEDV--E 57
           K Y  YK    +W+G IP HW  + IKR  +    R +    D I       G+  V  +
Sbjct: 2   KKYESYKPMKEKWLGDIPSHWDALRIKRIFQERKERNNPVTTDFILSLTAKQGVVPVAEK 61

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
            G G   PKD      D S  +I  +  +L   +      A ++ + G  S  +  L P+
Sbjct: 62  EGVGGNKPKD------DLSKYNICRENDLLVNCMNVVSGSAGVSKWVGAISPVYYALYPR 115

Query: 118 D--------------------VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNI 157
           D                     L  L +G L+    T ++  +    +M +     + N+
Sbjct: 116 DEEACNIWYYHQIFRLITFQRSLLGLGKGILMHESSTGKLNTVRMRISMDY-----LNNV 170

Query: 158 PMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKM 217
            +P+PP  EQ  I   +  +  +I+ +I+ + + I  + E     V+  VT G+  + ++
Sbjct: 171 VLPLPPRDEQDQIVRYLDWQISKINKMISNKRKQISRINEHLVFAVNEAVTHGIRNE-QL 229

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYG-NIIQKLETRNMGLK 276
           K+SGI W+G +P +W       L  E N +N +  E+ +L+ S    +I   +  +    
Sbjct: 230 KESGIFWMGKIPVNWNPIKIKWLFDETNERNIEC-EAELLTFSRKRGLIPFSDASDKEPS 288

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSA--QVMERGIITSAYMAVKPHG---IDST 331
                 Y++V PG++      L+N  ++       V   G ++  Y    P     ++  
Sbjct: 289 ASDLSNYRLVSPGQL------LENRMQAWSGMFICVTREGCVSPDYSVFNPSKDRYVNVK 342

Query: 332 YLAWLMRS----YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETA 387
           +  ++ R+             +GSG  + L       +  + PP +EQ  I   ++    
Sbjct: 343 FYEYVFRNPLQVEQFANASRGVGSGFNR-LYTPSFGAIYTVYPPKEEQDAIVEYLDGLKD 401

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           +     + IE  I +L E +   ++ AV+G+ID+R 
Sbjct: 402 KYKSATDVIESEIEVLHEIKDRLVSDAVSGKIDVRN 437


>gi|325662102|ref|ZP_08150720.1| hypothetical protein HMPREF0490_01458 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471551|gb|EGC74771.1| hypothetical protein HMPREF0490_01458 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 435

 Score = 84.7 bits (208), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 100/441 (22%), Positives = 194/441 (43%), Gaps = 50/441 (11%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES-----GKDIIYIGLEDVESGTGKYLP 65
           KDSG++W+G IP  WK + ++      T  T+        +++IY   ED        L 
Sbjct: 6   KDSGIKWVGEIPSDWKALKLRYICDKITDYTASGSFASLAENVIYRDYEDYAM-----LV 60

Query: 66  KDGN-SRQSDTSTVSI------------FAKGQILYGKLGP----YLRKAIIADFDGICS 108
           +  + S + +TS V +               G+++   +G     YL + I        +
Sbjct: 61  RTADLSNKRETSKVYVDEHAYNYLSNSNLFGGEVILPNIGSVGEVYLYQPIYER--ATLA 118

Query: 109 TQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
              +++Q  + + + L  +  +      ++ +    T    +   + N+ + IPP  + +
Sbjct: 119 PNAIMIQAPEEVEKFLYYYFSTYGAFDDLKNLGNATTQIKFNKTQLRNLKVVIPPKEKML 178

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
            I   +     +I++ +T   + I+ L+E K+++V   V+KG+    ++KD+  +    +
Sbjct: 179 KINCFLDRRCEKIESFVTVVQQQIDTLEELKRSVVYEAVSKGIKK-AELKDTDSDVWAKI 237

Query: 229 PDHWE---VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQI 285
           P  W+   VK  F +V  +  K       +ILS++   +  K  + N G   ++Y  YQI
Sbjct: 238 PKDWQLVDVKYLFEIVKRIAGKEG----IDILSVTQQGLKVKDISSNEGQIADNYSGYQI 293

Query: 286 VDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST---YLAWLMRSYDL 342
           V P + V   +DL        +      G+ +  Y   +     +    Y  ++M+   +
Sbjct: 294 VYPTDYVMNHMDLLTGWVDCSTM----FGVTSPDYRVFRLMDKANNSLRYYKYVMQCCYM 349

Query: 343 CKVFYAMGSGL----RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE-KIE 397
           C++FY++G G+    R  L+        V  PP+KEQ  I + I  + + I+ L+  KIE
Sbjct: 350 CRIFYSLGQGVSTLGRWRLQTSSFLNFKVPAPPLKEQEIIADYIEEKVSGIERLINLKIE 409

Query: 398 QSIVLLKERRSSFIAAAVTGQ 418
           Q  V L++ + + IA  VTG+
Sbjct: 410 QQRV-LEDYKKTLIADYVTGK 429


>gi|256375104|ref|YP_003098764.1| restriction modification system DNA specificity domain protein
           [Actinosynnema mirum DSM 43827]
 gi|255919407|gb|ACU34918.1| restriction modification system DNA specificity domain protein
           [Actinosynnema mirum DSM 43827]
          Length = 442

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 117/450 (26%), Positives = 190/450 (42%), Gaps = 67/450 (14%)

Query: 21  IPKHWKVVPIKRFTK-LNTGRTSE----------SGKDIIYIGLE----DVESGTGKYLP 65
           I   W   P+KR T  LN G   E          S     Y GL+       +  G    
Sbjct: 9   ISDTWTTSPLKRITSVLNRGSAPEYVDESPVRVISQAANQYGGLDWSRTRFHNFNGDPTK 68

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLR--KAIIADFDGICSTQFLVLQPKDVLPEL 123
             G+ +++D   + I + G    G++G +      I    DG  +   + ++   V P  
Sbjct: 69  LKGHLQEND---IIINSTGTGTLGRVGYFTEPLNGIPCMADGHVT--VVRVKKHKVNPRF 123

Query: 124 LQGWLLSIDVTQRIEA-ICEGATMS-HADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           +  WL S    + I + +  GAT     +   + +  +P PP++EQ  I + + AET  I
Sbjct: 124 VYYWLTSKPFQEYIHSSLAIGATNQIELNRDRLSDTHIPNPPISEQQRIVDFLEAETAHI 183

Query: 182 DTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW-EVKPFFAL 240
           D LI  + R +E L E++ A ++  V+         + S + W+  +P  W EV+   +L
Sbjct: 184 DRLIETQNRVLEKLAERRMAGITQAVSG--TDQTGTRPSSLTWLEKIPSTWKEVR--LSL 239

Query: 241 VTELNRKNTK-------LIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVF 293
           +  +   +T         ++  I  ++ G + Q    RN  L+ + +ET + +       
Sbjct: 240 IARMGSGHTPSRSHPEWWVDCTIPWITTGEVRQ---VRNDRLE-DLHETREKISE----- 290

Query: 294 RFIDLQNDKRSLRSA--------------QVMERGIITSAYMAVKPHG--IDSTYLAWLM 337
             + L N    LR A               VM   + TS        G  ++  YL W +
Sbjct: 291 --LGLANSAAELRPAGTVVLCRTASAGYSAVMGTDMATSQDFVTWTCGPRLNPYYLLWCL 348

Query: 338 RSY--DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           R+   DL     AMGS   +++   D++ L + +PPI EQ  I   I  + ARID L + 
Sbjct: 349 RAMRPDLLGRL-AMGS-THKTIYVPDLQMLRIPLPPIGEQQKIVQQIREQNARIDRLADA 406

Query: 396 IEQSIVLLKERRSSFIAAAVTGQIDLRGES 425
           +   + LL ERR + I AAVTGQID+   S
Sbjct: 407 VRLQVALLAERRQALITAAVTGQIDVSTAS 436


>gi|134097471|ref|YP_001103132.1| restriction modification system DNA specificity domain-containing
           protein [Saccharopolyspora erythraea NRRL 2338]
 gi|133910094|emb|CAM00207.1| putative restriction modification system DNA specificity domain
           [Saccharopolyspora erythraea NRRL 2338]
          Length = 411

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 84/328 (25%), Positives = 142/328 (43%), Gaps = 22/328 (6%)

Query: 105 GICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
           G+CS        +      L  WL S    +R++A+  G T      + +G +P P   L
Sbjct: 85  GLCSVSATGCDAR-----FLWWWLHS--AGERLDAVSTGTTYRAVTGEDVGMLPFPRVSL 137

Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
            EQ  I + + AET RID L   R R +++L+EK    V Y   +G       + SG+ W
Sbjct: 138 EEQRRIADFLDAETTRIDKLSALRERQLDILEEKAMRRV-YDTVRGTGVVGARRPSGLSW 196

Query: 225 VGLVPDHWEVKP---FFA------LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGL 275
           +G VP HW V     +F       L  E  R +       + ++ +G ++   E   M  
Sbjct: 197 LGSVPVHWRVAAVSHYFEVELGKMLNQERARGDHLRPYLRVANVQWG-VVDTTELAMMDF 255

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDST-YLA 334
            PE  + Y++  PG+++         + ++ S ++ E      A   ++P G++ST +L 
Sbjct: 256 PPEEQKRYRL-QPGDLLVNEGGSWPGRAAVWSGEI-EEIYYQKALHRIRPRGMESTWWLY 313

Query: 335 WLMRSYDLCKVFYAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLV 393
           + + + +  KVF   G S     L  E ++      P + EQ      +    A+   + 
Sbjct: 314 FCLVAAERMKVFQVQGNSSTMTHLTREQLRPQRFPFPDLAEQEQAVERLKDAEAKDRQIR 373

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQIDL 421
             + +    L ERR + I AAVTG+ D+
Sbjct: 374 RVLSRQQATLAERRQALITAAVTGEFDV 401


>gi|302380080|ref|ZP_07268555.1| type I restriction modification DNA specificity domain protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|302312100|gb|EFK94106.1| type I restriction modification DNA specificity domain protein
           [Finegoldia magna ACS-171-V-Col3]
          Length = 422

 Score = 83.6 bits (205), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 109/454 (24%), Positives = 187/454 (41%), Gaps = 84/454 (18%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-------SESGKDIIYIGLEDVESGTGKY 63
           KDSG++WIG IP+ W++   KR++K   G T         + K+ I +     E     Y
Sbjct: 6   KDSGIEWIGEIPEDWEISKFKRYSKSAMGNTILKTDLEENNNKETIPVYSATQEDVVFGY 65

Query: 64  LPKDGNSRQSDTSTVSIFAKGQ-ILYGKLGPYLRKA-----IIADFDGI-------CSTQ 110
           + ++  +     + + I A+G  I + KL PY +       I +  + I       CS  
Sbjct: 66  IDENNVTVILKKNNLVIPARGNSIGFTKLVPYAKATCTQTTIFSRLNNINEKFVYYCSIA 125

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           F     KD   E  Q  +  I V Q                  + N  +PI  + EQ  I
Sbjct: 126 F-----KDSWFEFDQTAIPQITVQQ------------------VENNNIPICSIEEQCKI 162

Query: 171 REKI---IAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
              +   +     I  +IT +I   E L+  K+++++  VTKGL+ +V+MKDSGIEW+G 
Sbjct: 163 TNFLSNKLENVKNIKIIITNQI---ENLENYKKSVITEAVTKGLDKNVEMKDSGIEWIGE 219

Query: 228 VPDHWE--------------VKPFF---ALVTELNRK--NTKLIESNILSLSYGNIIQKL 268
           +P HW+              + P +    L   +N+   +    +SN+   S   I + L
Sbjct: 220 IPKHWDLIKLKFIAHSISKGISPHYVEETLTPVVNQATFSKGFFDSNLKYCSEKPIGEGL 279

Query: 269 ETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI 328
              N  L   +         G ++ +    +   + L S  V        AY+  K   I
Sbjct: 280 LKMNDVLLATT--------GGGVLGKTYYFEEKGKYLASTDV--------AYIRNKDKYI 323

Query: 329 DSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
                  L  +YDL    +A GS  +  L+ + +  + + +P   E   I + ++V    
Sbjct: 324 SKFIYYILSVNYDLLNGIFAKGSTNQTHLQMDLLSNMHIPLPNQNELSKIISKLDVVNTN 383

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           ID  +   ++ +  L+E + S I   VTG+ +++
Sbjct: 384 IDDSIAIKQKQLDTLEEYKKSLIYEYVTGKKEVK 417



 Score = 41.6 bits (96), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 46/207 (22%), Positives = 88/207 (42%), Gaps = 10/207 (4%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFT-KLNTGRTSESGKDIIYIGLEDVESGTGKYLPKD 67
           + KDSG++WIG IPKHW ++ +K     ++ G +    ++ +   +       G +   D
Sbjct: 208 EMKDSGIEWIGEIPKHWDLIKLKFIAHSISKGISPHYVEETLTPVVNQATFSKGFF---D 264

Query: 68  GNSRQSDTSTV--SIFAKGQILYGKL-GPYLRKAIIADFDG--ICSTQFLVLQPKDVLPE 122
            N +      +   +     +L     G  L K    +  G  + ST    ++ KD    
Sbjct: 265 SNLKYCSEKPIGEGLLKMNDVLLATTGGGVLGKTYYFEEKGKYLASTDVAYIRNKDKYIS 324

Query: 123 LLQGWLLSIDVTQRIEAICEGAT-MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
               ++LS++         +G+T  +H     + N+ +P+P   E   I  K+      I
Sbjct: 325 KFIYYILSVNYDLLNGIFAKGSTNQTHLQMDLLSNMHIPLPNQNELSKIISKLDVVNTNI 384

Query: 182 DTLITERIRFIELLKEKKQALVSYIVT 208
           D  I  + + ++ L+E K++L+   VT
Sbjct: 385 DDSIAIKQKQLDTLEEYKKSLIYEYVT 411



 Score = 40.4 bits (93), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 14/22 (63%), Positives = 18/22 (81%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPF 237
           KMKDSGIEW+G +P+ WE+  F
Sbjct: 4   KMKDSGIEWIGEIPEDWEISKF 25


>gi|288932536|ref|YP_003436596.1| restriction modification system DNA specificity domain protein
           [Ferroglobus placidus DSM 10642]
 gi|288894784|gb|ADC66321.1| restriction modification system DNA specificity domain protein
           [Ferroglobus placidus DSM 10642]
          Length = 421

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 58/176 (32%), Positives = 86/176 (48%), Gaps = 25/176 (14%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDII----------YIGLEDVES 58
           ++KDS    IG +P+ W+VV +        G+ +E  K+I+          Y+GLE V S
Sbjct: 219 RFKDSE---IGKVPEDWEVVKL--------GKVAEQRKEIVDPTEVDPVTPYVGLEHVNS 267

Query: 59  GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
           G  K L   G + +  +S    + +  ILYGKL PYL KA+I++ +G+CST F+V++ K 
Sbjct: 268 GETK-LSNFGKAEEVVSSKYRFYIR-DILYGKLRPYLDKAVISNINGVCSTDFIVMRTKR 325

Query: 119 --VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
              +P+ L   L +        A   G       W  I     P+PPL EQ  I E
Sbjct: 326 DYTIPDFLIYVLHTKRFIDYSTAGMTGTNHPRTSWNWIAKFEFPLPPLQEQKAIAE 381


>gi|312110993|ref|YP_003989309.1| restriction modification system DNA specificity domain protein
           [Geobacillus sp. Y4.1MC1]
 gi|311216094|gb|ADP74698.1| restriction modification system DNA specificity domain protein
           [Geobacillus sp. Y4.1MC1]
          Length = 409

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/192 (36%), Positives = 99/192 (51%), Gaps = 18/192 (9%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           YIGLE +  GT + L   G S +  TST S F+KG IL+GKL PY RK +   F+G+CST
Sbjct: 30  YIGLEHIGQGTLR-LISVGKSNEV-TSTKSYFSKGDILFGKLRPYFRKVVRPKFNGVCST 87

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRI----EAICEGATMSHADWKGIGNIPMPIPPLA 165
             LVL  K+   +  Q +L  +  +Q +     A   G  M  ADWK + N+ + IP   
Sbjct: 88  DILVLTSKNPR-KFNQTFLFYLMASQEMIDLATASSSGTKMPRADWKVLQNLEISIP--- 143

Query: 166 EQVLIREKI--IAETVRIDTLITERIRFIELLKEKKQALVSY-IVTKGLNPDVKMKDSGI 222
           E V  +E+I  I ET  ID  I   IR  + L+E    L  +  V  G   D +  +S +
Sbjct: 144 EDVNEQERIGKILET--IDDKIDINIRMNKTLEEMAMTLYKHWFVDFGPFQDEEFVESEL 201

Query: 223 EWVGLVPDHWEV 234
              G++P  W+V
Sbjct: 202 ---GMIPKGWKV 210


>gi|91215847|ref|ZP_01252816.1| putative type I restriction enzyme (specificity subunit)
           [Psychroflexus torquis ATCC 700755]
 gi|91185824|gb|EAS72198.1| putative type I restriction enzyme (specificity subunit)
           [Psychroflexus torquis ATCC 700755]
          Length = 426

 Score = 81.3 bits (199), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 105/446 (23%), Positives = 184/446 (41%), Gaps = 59/446 (13%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD---------IIYIGLEDVE 57
           Y  YKDSG++W+G IP HW+V  +K    L  G+ +   ++           ++   DV 
Sbjct: 4   YDTYKDSGIEWLGEIPVHWEVKRVKEIFNLVRGKFTHRPRNDQRMYNNGTFPFLQTGDV- 62

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
           + + KY+ +       +   VS   K   L   +   +    +  FD       +    K
Sbjct: 63  AKSSKYVLQYKQVLNENGIKVSRQFKKGTLVMTIAANIGDVALLGFDAYFPDSLVAFNTK 122

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
             +      +LLS+  ++ ++ +    T  + + + + ++    PPL+EQ +I   +  +
Sbjct: 123 HNIN--FYYYLLSVTKSE-LDTVKITNTQDNLNLERLNSLLKICPPLSEQTIIANYLDKK 179

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDV-----KMKDSGIEWVGLV---- 228
           T  ID  I    +  +  KE +++L++  VT GL+ +      ++KD G  + GL     
Sbjct: 180 TTAIDQKINLLTKKTDKYKELRKSLINQTVTDGLDKNTIWKTYRLKDIGQIYSGLSGKNG 239

Query: 229 --------PDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPE-- 278
                   P++    PF       N  N   ++   LS     II   E +N   K +  
Sbjct: 240 DDFKKEKDPNNRGFIPF------TNIANNTYLDVEHLSKV---IISPTENQNKVQKNDLF 290

Query: 279 ---SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAW 335
              S E Y+ +    +      L+ D          +   IT+         +D+ ++ +
Sbjct: 291 FLMSSEGYEDIGKSAV------LKEDIPETYLNSFCKGFRITNT-------NVDAFFINY 337

Query: 336 LMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIK-EQFDITNVINVETARIDVLV 393
           L+ S D        G G  R +LK E V    + +P  K EQ  I N ++ +T+ ID +V
Sbjct: 338 LLLSDDNRNKMVIQGKGFTRINLKIEKVNNFSITIPSTKAEQTAIANYLDEKTSTIDAIV 397

Query: 394 EKIEQSIVLLKERRSSFIAAAVTGQI 419
             IE+ I  LKE R + I   VTG+I
Sbjct: 398 SNIERQINHLKELRKTVINDVVTGKI 423


>gi|303229059|ref|ZP_07315865.1| type I restriction modification DNA specificity domain protein
           [Veillonella atypica ACS-134-V-Col7a]
 gi|302516270|gb|EFL58206.1| type I restriction modification DNA specificity domain protein
           [Veillonella atypica ACS-134-V-Col7a]
          Length = 435

 Score = 80.5 bits (197), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 100/444 (22%), Positives = 185/444 (41%), Gaps = 52/444 (11%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTG---RTSESGKDIIY--IGLEDVESGTGKY 63
           + KDSGV WIG IP +WK + +K  +KL  G   ++ +   D  Y  + + D+ +     
Sbjct: 4   EMKDSGVPWIGKIPVNWKTIRLKYISKLINGFAFKSQDLKADGHYKVVRIGDLNNNKINL 63

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPEL 123
               G     +     I+  G +L    G  + K   AD +  C     V   + +   L
Sbjct: 64  EDCLGVDSVDNYRDYKIYM-GDVLVALSGATVGKVAFADNNIECYINQRVGIIRSLWGRL 122

Query: 124 LQGWLLSID-VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
           +   + S+D   + +++    +   +   + IG I +PI        I   +  +  +ID
Sbjct: 123 IFH-IFSLDKFIENLKSCLNDSAQPNLSIEDIGRISIPIYDKNTIKRIVRYLDIKCAQID 181

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
           T+I +    IE L+E K+A+++  V KGL+  V+M D GIEW+  +P+HW++        
Sbjct: 182 TIIAKEQSVIEKLQEYKRAIITNAVVKGLDLTVEMADRGIEWIDSIPNHWKI-------- 233

Query: 243 ELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDK 302
                  +LI S  +    G   + L+      +   + +   +   ++V+  ++  ND 
Sbjct: 234 ------NRLIFSAYIRARLG--WKGLKADEYTSEGHPFLSAVNIQNDKLVWEDLNFINDN 285

Query: 303 RSLRSAQVMER-----------GIITSAYMAVKPHG----------------IDSTYLAW 335
           R   S ++              GI   A +   P+G                ++S YL +
Sbjct: 286 RYDESPEIKLELGDLLLVKDGAGIGKCAIVDQLPYGTATTNSSLGVITPYSELNSMYLYY 345

Query: 336 LMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
              S         + +G+    L   ++K + V++PP  EQ  I   ++ + + +D ++ 
Sbjct: 346 FFESAIFQNYISRIKNGMGVPHLTQGNLKNIMVVIPPYCEQEAIVAYLDDKCSNLDSIIL 405

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQ 418
           K +  I  L E + S I   VTG+
Sbjct: 406 KKQSLIDKLIEYKKSLIYEVVTGK 429


>gi|150017995|ref|YP_001310249.1| restriction modification system DNA specificity subunit
           [Clostridium beijerinckii NCIMB 8052]
 gi|149904460|gb|ABR35293.1| restriction modification system DNA specificity domain [Clostridium
           beijerinckii NCIMB 8052]
          Length = 469

 Score = 80.5 bits (197), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 112/490 (22%), Positives = 202/490 (41%), Gaps = 93/490 (18%)

Query: 3   HYKAYPQYKDSGVQWIGAIPKHWKVVPIKRF--------------TKLNTGRTSESGKDI 48
            Y++  + KDSGV+WIG IP+ W+V  IK                + L +    E+G+  
Sbjct: 4   RYRSEEEMKDSGVKWIGKIPRDWEVSKIKYIKSPDKNSFVDGPFGSNLKSEHFIENGE-- 61

Query: 49  IYIGLEDVES--GTGKYLPKDG----NSRQSDTSTVSIFAKGQILYGKLGPYL------- 95
           +Y+    +ES   T   L  D     ++   +T   S   +  I+  K+G          
Sbjct: 62  VYV----IESNFATQGILKLDSLKKISTEHFETIKRSEVKENDIVIAKIGAQFGLSNILP 117

Query: 96  ---RKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWK 152
              +KA+++      ++  L +  +    + +   LL I     ++ I            
Sbjct: 118 RIDKKAVVSG-----NSLKLSVDKQKSNTQYIHYQLLHIKNNGTLDLIVSTTAQPAISLG 172

Query: 153 GIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLN 212
            + NI + +P +  Q  I + +  +T ++D++I+++   I++L+E K++L+S  VT  + 
Sbjct: 173 DMNNINIVLPNVQRQDKIVKFLNEKTAQVDSIISKKEALIQILEEAKKSLISDAVTGKVK 232

Query: 213 -------------PDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN--RKNTKLIESNIL 257
                           +MKDSG++W+G VP  W+VK    L    N   K+         
Sbjct: 233 VVKTSDGYELVERKKEEMKDSGVKWLGDVPKEWDVKRLRFLGNLQNGISKSGDEFGFGYP 292

Query: 258 SLSYGNIIQKLETRNM--GLKPESYETYQI--VDPGEIVFRFIDLQNDKRSLRSAQVMER 313
            +SYG++ + +       GL   S    +I  V  G++ F          +  S  V E 
Sbjct: 293 FVSYGDVYKNISIPKFVNGLVNSSLNDRRIYSVLEGDVFF----------TRTSETVDEI 342

Query: 314 GIITSAYMAVKPHGIDSTYLAWLMR-----------------SYDLCKVFYAMGSGL--R 354
           G  ++    +     D+T+  +L+R                   DL + F+     L  R
Sbjct: 343 GFASTCLNTI----TDATFAGFLIRFRPFKDKLYKGFSKYYFRCDLNRKFFVKEMNLVTR 398

Query: 355 QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAA 414
            SL    +  L V +P  KEQ +I + +  +   I+  + K+   I  LKE + + I+ A
Sbjct: 399 ASLSQNLLNNLAVALPLYKEQQEIYSALEFKVGGIECSINKLRCQIQKLKEAKQALISEA 458

Query: 415 VTGQIDLRGE 424
           VTG+I +  E
Sbjct: 459 VTGKIKILDE 468


>gi|160903326|ref|YP_001568907.1| restriction modification system DNA specificity subunit [Petrotoga
           mobilis SJ95]
 gi|160360970|gb|ABX32584.1| restriction modification system DNA specificity domain [Petrotoga
           mobilis SJ95]
          Length = 433

 Score = 79.3 bits (194), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 47/151 (31%), Positives = 74/151 (49%), Gaps = 3/151 (1%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           IG +P+ W+V       ++       S  + IY+GLE +ESG  K L K G S+   ++ 
Sbjct: 234 IGLVPEEWEVKNFGEIVEIRKEIIDPSNGNYIYVGLEHIESGNIK-LRKTGLSKGVKSAK 292

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRI 137
             I+    ILY KL PYL K I+ + +GICST  LV + K+ +      +L   +  +  
Sbjct: 293 YKIYP-NDILYAKLRPYLDKGILVEQEGICSTDLLVFKAKENVYASFIAYLEHTNYFREY 351

Query: 138 E-AICEGATMSHADWKGIGNIPMPIPPLAEQ 167
                 G       W+ +  + +P+PPL+EQ
Sbjct: 352 AIKTMTGVNHPRTSWRALSQLTIPLPPLSEQ 382



 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 103/444 (23%), Positives = 199/444 (44%), Gaps = 64/444 (14%)

Query: 9   QYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTS-----ESGKDIIYIGLEDVES----- 58
           +YK++    +G +PK W+VV +   ++L  G+T      E  K    I ++D E+     
Sbjct: 10  EYKETE---LGLLPKDWEVVRLGEVSELQQGKTPKRDDYEDYKGYRIIKVKDYENENKIS 66

Query: 59  ----GTGKYLPKDGNSR----QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
               G   ++  D   R    + D+  +S      I+  K+G Y+++  I         +
Sbjct: 67  NIIKGDRSFVKTDFGERCRIKEGDSLILSAAHSSNIVGQKIG-YVKE--IPSQKTFFVAE 123

Query: 111 FLVLQPK-DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
            + ++PK +++P       LS+ +      I E     H   K +G I +P+PPL+EQ  
Sbjct: 124 LIRVRPKKNIIPYFC---FLSLILMSSRNQIREEVKGGHLYPKNLGKIRIPLPPLSEQKK 180

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNP-------DVKMKDSGI 222
           I    +  +V+     TE +  I+  KE K+++++++ T G  P        V +K++ I
Sbjct: 181 I--AYVLSSVQEAKEKTEDV--IKATKELKKSMMNHLFTYG--PVSLEEVEKVPLKETEI 234

Query: 223 EWVGLVPDHWEVKPFFALVTELNRK-----NTKLIESNILSLSYGNIIQKLETRNMGLKP 277
              GLVP+ WEVK F  +V E+ ++     N   I   +  +  GNI  +    + G+K 
Sbjct: 235 ---GLVPEEWEVKNFGEIV-EIRKEIIDPSNGNYIYVGLEHIESGNIKLRKTGLSKGVKS 290

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWL 336
             Y+ Y    P +I++  +    DK  L    V + GI ++  +  K    + ++++A+L
Sbjct: 291 AKYKIY----PNDILYAKLRPYLDKGIL----VEQEGICSTDLLVFKAKENVYASFIAYL 342

Query: 337 MRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
             +    +      +G+      +  + +L + +PP+ EQ  I ++++     ID  +E 
Sbjct: 343 EHTNYFREYAIKTMTGVNHPRTSWRALSQLTIPLPPLSEQKKIASILSA----IDQKIEA 398

Query: 396 IEQSIVLLKERRSSFIAAAVTGQI 419
            E     L++   S +   +T +I
Sbjct: 399 EESKKKALEDLFKSLLHNLMTAKI 422


>gi|238854454|ref|ZP_04644794.1| type IC specificity subunit [Lactobacillus jensenii 269-3]
 gi|282932599|ref|ZP_06338020.1| type IC specificity subunit [Lactobacillus jensenii 208-1]
 gi|313472061|ref|ZP_07812553.1| type I restriction-modification system, specificity subunit
           [Lactobacillus jensenii 1153]
 gi|238832947|gb|EEQ25244.1| type IC specificity subunit [Lactobacillus jensenii 269-3]
 gi|239530090|gb|EEQ69091.1| type I restriction-modification system, specificity subunit
           [Lactobacillus jensenii 1153]
 gi|281303295|gb|EFA95476.1| type IC specificity subunit [Lactobacillus jensenii 208-1]
          Length = 390

 Score = 79.3 bits (194), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 96/383 (25%), Positives = 163/383 (42%), Gaps = 50/383 (13%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG 84
           WK      F+   T  ++    D   I  E++ SG GK       S+ +   +   F KG
Sbjct: 14  WKNKKFLTFSSKITKNSTSDDIDFPRIEFENIVSGEGKL--AQNRSKLNHIKSGIKFDKG 71

Query: 85  QILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGA 144
            IL+GKL PYL+   +A+F G+    F V++ KD        +L+   + +++     G 
Sbjct: 72  DILFGKLRPYLKNWWLAEFPGVAVGDFWVIRAKD--NRYFLYYLIQAPLFEKVSNYTTGT 129

Query: 145 TMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVS 204
            M  +DW  + N    +P + EQ    EKI     ++D+L++ + R +EL  +  +A+ +
Sbjct: 130 KMPRSDWNYVSNTFFKLPKIDEQ----EKIGRILDKVDSLLSLQHRKMELENQTSKAIYN 185

Query: 205 YIVTK--------GLNPDVKMKDSGIEWVGLVPD------HWEVKPFFALVTELNRKNTK 250
           Y+  K             V +K+ G  + GL         H + K     +T LN     
Sbjct: 186 YLFDKNKPFYFKDNKTKKVFLKELGTTYSGLSGKNKTDFGHGKAK----YITYLNVNKNT 241

Query: 251 LIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV 310
           +   N+L L     I+  + +N  L             G+I+F       ++  L S   
Sbjct: 242 IANHNLLDL-----IEIDKKQNEVLN------------GDILFTISSETPEEVGLASLWP 284

Query: 311 MERGII--TSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLP 366
            +   I   S     +P+  I++ +LA+ +RS  + K  Y +  G+ R +L  + V  L 
Sbjct: 285 YDDTNIYLNSFCFGFRPNSKINNLWLAYELRSLKIRKNMYKLAQGISRYNLSKKSVLNLQ 344

Query: 367 VLVPPIKEQ-FD--ITNVINVET 386
           V VP   EQ FD     +IN++T
Sbjct: 345 VDVPSDAEQNFDSKFVKLINIQT 367


>gi|189423911|ref|YP_001951088.1| restriction endonuclease S subunits-like protein [Geobacter lovleyi
           SZ]
 gi|189420170|gb|ACD94568.1| restriction endonuclease S subunits-like protein [Geobacter lovleyi
           SZ]
          Length = 386

 Score = 79.3 bits (194), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/175 (32%), Positives = 82/175 (46%), Gaps = 19/175 (10%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDII--YIGLEDVESGTGKYLPKD------GNSRQSDTS 76
           W+ V      +L+  R+S+   D    YIGLE ++       P+D      GN     T 
Sbjct: 10  WQKVKFGDVVRLSKERSSDPLADGYERYIGLEHID-------PEDLRVRRWGNVADGVTF 62

Query: 77  TVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ---PKDVLPELLQGWLLSIDV 133
           T S+F  GQ+L+GK   Y RK  +ADF G+CS    VL+   PK +LPELL     +   
Sbjct: 63  T-SVFKPGQVLFGKRRAYQRKVAVADFAGVCSGDIYVLESKDPKKLLPELLPFICQTEAF 121

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITER 188
            Q       G+     +W  + +    +PPL EQ  I E ++A    ID L++ R
Sbjct: 122 FQHAVGTSAGSLSPRTNWTSLADFEFALPPLEEQRRIVELLLAVEETIDNLVSAR 176


>gi|168232879|ref|ZP_02657937.1| type I restriction enzyme EcoKI specificity protein [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|194472515|ref|ZP_03078499.1| type I restriction enzyme EcoKI specificity protein [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194458879|gb|EDX47718.1| type I restriction enzyme EcoKI specificity protein [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|205332898|gb|EDZ19662.1| type I restriction enzyme EcoKI specificity protein [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
          Length = 486

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 98/207 (47%), Gaps = 4/207 (1%)

Query: 19  GAIPKHW---KVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75
           G +P+ W   ++  I  + K      S+   D   + LED+E  + K L     S +   
Sbjct: 4   GKLPEGWVDTQLGNIVDYGKATKRVLSDVNDDTWVLELEDIEKESSKLLSTIRASERPFK 63

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELLQGWLLSIDVT 134
           ST + F +G +LYGKL PYL K IIA  DG+C+T+ + L  +     + +  WL S    
Sbjct: 64  STKNSFKRGDVLYGKLRPYLNKIIIAKEDGVCTTEIIPLCAEPSCCNKYIFYWLKSSTFQ 123

Query: 135 QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIEL 194
             +  +  G  M           P+ + PLAEQ +I EK+     +ID+      +  ++
Sbjct: 124 GYVNDVSYGVNMPRLGTADGLKAPLRLAPLAEQKIIAEKLDTLLAQIDSTKARLEQIPQI 183

Query: 195 LKEKKQALVSYIVTKGLNPDVKMKDSG 221
           LK  +QA+++  V+  L  + +M ++ 
Sbjct: 184 LKRFRQAVLAAAVSGNLTAEWRMNNNS 210


>gi|146300449|ref|YP_001195040.1| restriction modification system DNA specificity subunit
           [Flavobacterium johnsoniae UW101]
 gi|146154867|gb|ABQ05721.1| restriction modification system DNA specificity domain protein
           [Flavobacterium johnsoniae UW101]
          Length = 267

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 124/255 (48%), Gaps = 30/255 (11%)

Query: 187 ERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNR 246
           ++ R IELL EKK+A++   + KGL P+V MKDSGIEW G +P+HW+V     L      
Sbjct: 22  KKTRLIELLDEKKKAVIIQNIIKGLAPNVAMKDSGIEWFGEIPEHWKVVKLKYL------ 75

Query: 247 KNTKLIESNILSLSYGNIIQKLETR--NMGLKPESYETYQIVDPG--EIVFRFIDLQNDK 302
             +K I++      Y   I++L     N     +  E +  V+    ++ F  ++  N+ 
Sbjct: 76  --SKNIDTGSTPNGYDIPIEELNENVWNWFTPGDFNEDFNFVNESKRKLSFEVVE-DNNV 132

Query: 303 RSLRSAQVMERGI-ITSAYMAVKPHGIDSTYLAWLMR-SYDLCKVF--YAMGSGLRQSLK 358
           R   S  VM  GI  T   +AV      +     ++  + D+ K+F  Y++ + ++ S  
Sbjct: 133 RLYDSNSVMFVGIGATLGKIAVTDTNFYTNQQINIIELNNDINKMFVAYSLSATIKISKM 192

Query: 359 FEDVKRLPVL-----------VPPIKEQFDITNVI-NVETARIDVLVEKIEQSIVLLKER 406
             +   LP+L           +P + EQ  +   + N+     ++   KI  SI LLKE+
Sbjct: 193 LANSATLPILNQQKLGDIQIPIPDLNEQILVVERLENIYFNHFNI-ANKISTSIELLKEK 251

Query: 407 RSSFIAAAVTGQIDL 421
           R++ I+A + G+I+L
Sbjct: 252 RTAIISATINGEINL 266



 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 114/223 (51%), Gaps = 27/223 (12%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTSESGKDIIYIGLEDVESGTGKYL-PKDG 68
           KDSG++W G IP+HWKVV +K  +K ++TG T  +G D   I +E++      +  P D 
Sbjct: 53  KDSGIEWFGEIPEHWKVVKLKYLSKNIDTGSTP-NGYD---IPIEELNENVWNWFTPGDF 108

Query: 69  NSRQS--------------DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL 114
           N   +              + + V ++    +++  +G  L K  + D +   + Q  ++
Sbjct: 109 NEDFNFVNESKRKLSFEVVEDNNVRLYDSNSVMFVGIGATLGKIAVTDTNFYTNQQINII 168

Query: 115 QPKDVLPELLQGWLLSIDVTQRI-EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
           +  + + ++   + LS   T +I + +   AT+   + + +G+I +PIP L EQ+L+ E+
Sbjct: 169 ELNNDINKMFVAYSLS--ATIKISKMLANSATLPILNQQKLGDIQIPIPDLNEQILVVER 226

Query: 174 IIAETVRIDTL-ITERIRF-IELLKEKKQALVSYIVTKGLNPD 214
           +  E +  +   I  +I   IELLKEK+ A++S  +   +N D
Sbjct: 227 L--ENIYFNHFNIANKISTSIELLKEKRTAIISATINGEINLD 267


>gi|111026979|ref|YP_708957.1| type I restriction-modification system specificity subunit
           [Rhodococcus jostii RHA1]
 gi|110825518|gb|ABH00799.1| type I restriction-modification system specificity subunit
           [Rhodococcus jostii RHA1]
          Length = 391

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 101/438 (23%), Positives = 170/438 (38%), Gaps = 93/438 (21%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           +P  W V  ++R      G              ++VE   G Y P  G+  +   ++  +
Sbjct: 11  LPSGWVVAQMRRIATFRNG-----------ADYKEVEVTEGGY-PVYGSGGEFRRASQYL 58

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAI 140
           +    +L+G+ G   +  +++       T F      ++ P  L  +      T   +  
Sbjct: 59  YDGESVLFGRKGTIDKPLLVSGRFWTVDTMFFTELTSNIEPRYLHYYA----TTMPFDYY 114

Query: 141 CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQ 200
                +       +G   +P+PP+ EQ  I + +  ET RIDTLI E+ R IELL+E++ 
Sbjct: 115 STSTALPSMTQGELGGHRIPLPPITEQGAIADFLDRETARIDTLIREQRRLIELLRERRI 174

Query: 201 ALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS 260
           A+    V             G+ W           P         R  T LI++      
Sbjct: 175 AVAEGPVV------------GLSWS---------TPL--------RSVTALIQTG----P 201

Query: 261 YGNIIQKLETRNMGLKPESYET--YQIVDPGEIVFRFIDLQN------------DKRSLR 306
           +G+           LK + YET    +++P  +V   I+                + +LR
Sbjct: 202 FGS----------QLKSDEYETGGTPVINPSHLVMGRIEPDERVAVSASKASELGRHALR 251

Query: 307 SAQVM--ERGIIT-----------------SAYMAVKPHGIDSTYLAWLMRSY-DLCKVF 346
           +  V+   RG +                  SA + ++    D  +LA +  S  +   + 
Sbjct: 252 AGDVIAARRGELGRCAVVRAENTGFLCGTGSALIRLRETVADPEFLALVFSSRRNRDSLS 311

Query: 347 YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
            A       +L  + +  L + +PP+ EQ  I   +   T +ID L+ + E  I L KER
Sbjct: 312 LASVGATMDNLNADIIATLRIPMPPLPEQRRIVESVAEATTKIDTLITETESFIDLAKER 371

Query: 407 RSSFIAAAVTGQIDLRGE 424
           RS+ I AAVTGQID+R E
Sbjct: 372 RSALITAAVTGQIDVRDE 389


>gi|158337894|ref|YP_001519070.1| restriction modification system DNA specificity subunit
           [Acaryochloris marina MBIC11017]
 gi|158308135|gb|ABW29752.1| restriction modification system DNA specificity domain
           [Acaryochloris marina MBIC11017]
          Length = 295

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/282 (24%), Positives = 124/282 (43%), Gaps = 17/282 (6%)

Query: 150 DWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTK 209
           D+     +P+ IPP+ EQ  I E +  +TV +D  I  + R IELL+E+K  L++  VTK
Sbjct: 17  DYTDFKYLPLTIPPIDEQRRIVEFLDRKTVELDDAIATKQRLIELLQEQKAILINQAVTK 76

Query: 210 GLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN-------RKNTKLIESNILSLSYG 262
           GL+P+V M D GI  +  VP+HW++     L   L        R + +        +  G
Sbjct: 77  GLDPNVPMCDRGIHGLEKVPNHWKLCSVKRLTQILRGKFSHRPRNDARFYGGQYPFIQTG 136

Query: 263 NIIQ---KLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSA 319
           +I Q   ++   +  L    Y   +    G +V      +  + S+           ++ 
Sbjct: 137 DISQAGRRITKYSQTLNARGYAVSKEFPAGTVVMVITGAKTGEVSILGFNACFPD--SAV 194

Query: 320 YMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGS--GLRQSLKFEDVKRLPVLVPPIKEQFD 377
                P  + + +L ++   + + K      S    +++L  + +  L    PP++EQ  
Sbjct: 195 GFFPNPGEVSADFLYYM---FGVLKTRLDEVSIVSTQENLNVDRIGALYTACPPVEEQNQ 251

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           I + ++      +    + E+ I  L+E R   I+ AVTG+I
Sbjct: 252 IVDFLDNRLLGFETAQVRAEEQINKLQEFREILISHAVTGKI 293



 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 50/79 (63%)

Query: 342 LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
           + KV+Y MGSGLRQ+L + D K LP+ +PPI EQ  I   ++ +T  +D  +   ++ I 
Sbjct: 1   MLKVYYGMGSGLRQNLDYTDFKYLPLTIPPIDEQRRIVEFLDRKTVELDDAIATKQRLIE 60

Query: 402 LLKERRSSFIAAAVTGQID 420
           LL+E+++  I  AVT  +D
Sbjct: 61  LLQEQKAILINQAVTKGLD 79



 Score = 38.9 bits (89), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 45/208 (21%), Positives = 86/208 (41%), Gaps = 14/208 (6%)

Query: 12  DSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSES--------GKDIIYIGLEDVESGTGKY 63
           D G+  +  +P HWK+  +KR T++  G+ S          G    +I   D+ S  G+ 
Sbjct: 86  DRGIHGLEKVPNHWKLCSVKRLTQILRGKFSHRPRNDARFYGGQYPFIQTGDI-SQAGRR 144

Query: 64  LPKDGNSRQSDTSTVSI-FAKGQILYGKLGPYLRKAIIADFDGIC--STQFLVLQPKDVL 120
           + K   +  +    VS  F  G ++    G    +  I  F+     S       P +V 
Sbjct: 145 ITKYSQTLNARGYAVSKEFPAGTVVMVITGAKTGEVSILGFNACFPDSAVGFFPNPGEVS 204

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
            + L  ++  + +  R++ +   +T  + +   IG +    PP+ EQ  I + +    + 
Sbjct: 205 ADFLY-YMFGV-LKTRLDEVSIVSTQENLNVDRIGALYTACPPVEEQNQIVDFLDNRLLG 262

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVT 208
            +T        I  L+E ++ L+S+ VT
Sbjct: 263 FETAQVRAEEQINKLQEFREILISHAVT 290


>gi|126179043|ref|YP_001047008.1| restriction modification system DNA specificity subunit
           [Methanoculleus marisnigri JR1]
 gi|125861837|gb|ABN57026.1| restriction modification system DNA specificity domain
           [Methanoculleus marisnigri JR1]
          Length = 394

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 89/175 (50%), Gaps = 11/175 (6%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSES---GKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           +P+ W++V ++   K++    S     G+   YIGLE++ES TG+ +           S 
Sbjct: 6   LPEGWRLVKLEEVAKIDNKAVSPDEMRGELQNYIGLENIESNTGQLVSFSETLGDDIKSN 65

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLLSIDVTQ 135
              F +  ILYGKL PYL K  + DF G+CST  + ++P    ++ E L  +L + +   
Sbjct: 66  KFGFTEEHILYGKLRPYLNKVYLPDFAGVCSTDIIPIKPDSDLLIREFLGYFLRTPEFVS 125

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIR 190
            I A   GA +   + K + ++ +P+PP+  Q     KI+A  +   T  T+R+R
Sbjct: 126 MINAKSSGANLPRVNPKTLLDVYIPLPPIETQY----KIVA--ILEKTEATQRLR 174


>gi|330999089|ref|ZP_08322812.1| type I restriction modification DNA specificity domain protein
           [Parasutterella excrementihominis YIT 11859]
 gi|329575610|gb|EGG57144.1| type I restriction modification DNA specificity domain protein
           [Parasutterella excrementihominis YIT 11859]
          Length = 429

 Score = 77.4 bits (189), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 55/169 (32%), Positives = 81/169 (47%), Gaps = 7/169 (4%)

Query: 21  IPKHWKVV---PIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           IPK WK V    I  + K          +D   + LED+E  TG+ L K  N    +   
Sbjct: 44  IPKKWKWVRLDDIAPYGKCERIEACSFDRDTWLLNLEDIEKDTGRLLQK--NKIIKNQGA 101

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLLSIDVTQ 135
             +F KG +LY +L PYL K ++AD DG+C+T+ + L+PK+  +    L  +L S    Q
Sbjct: 102 KYLFNKGDVLYSRLRPYLNKVLVADEDGVCTTEIIPLKPKENTLSGSYLSFFLKSQYFVQ 161

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
              +   G  M         N  + +PPL EQ  I EK+ +   +IDT+
Sbjct: 162 YAVSQSYGVKMPRVGTATAKNALVALPPLDEQKRIVEKLESLFAKIDTI 210


>gi|269140413|ref|YP_003297114.1| type I restriction modification DNA specificity domain protein
           [Edwardsiella tarda EIB202]
 gi|267986074|gb|ACY85903.1| type I restriction modification DNA specificity domain protein
           [Edwardsiella tarda EIB202]
          Length = 441

 Score = 77.0 bits (188), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 97/434 (22%), Positives = 176/434 (40%), Gaps = 49/434 (11%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTS---ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSD 74
           +G IP+ W+VVP      + +G+ S   E    +  I  + +E+GTG+ + K     Q  
Sbjct: 23  VGVIPEDWEVVPFFDVVSIVSGQISPICEPYSSMTLIAPDHIETGTGRLISKKSAKEQGA 82

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDV 133
            S   +F  G  +Y K+ PYLRKAI A+FDG+CS     L+PK+ + P+ +   +L    
Sbjct: 83  ISGKYVFHAGDTIYSKIRPYLRKAIYANFDGLCSADMYPLRPKEGIEPKYILPLVLGNRF 142

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIE 193
           ++  E++   + +   +   I +    IP   E+      ++ +T  +       I  +E
Sbjct: 143 SKYAESVSVRSGIPKINRTEIADFLFVIPRQREEQTAIANVLFDTEAL-------IAALE 195

Query: 194 LLKEKKQALVSYIVTKGLN-----PDVKMKDSGI------EWVGLVPDHWEVKPF--FAL 240
            +  KKQA+ +  + + L      P   M + G         +G +P+ W V     F  
Sbjct: 196 QILAKKQAIKTAAMQQLLTGKTRLPQFAMWEDGTTKGYKKSELGEIPEDWVVTNIGQFTD 255

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD-----------PG 289
                   TK      +S  +G     + +  + LK        I D           P 
Sbjct: 256 CCAGGTPGTK------VSAYWGGTHPWMSSGELHLKQVHTVADYITDEGLANSSTKYVPK 309

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAW--LMRSYDLCKVFY 347
             V   +  Q   R   +   +E      +  A+ P    ST   +  L   Y+  +   
Sbjct: 310 NSVLVGLAGQGKTRGTVAINRIEL-CTNQSIAAIFPGEHHSTEFLFYNLDNRYEELRSL- 367

Query: 348 AMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
           + G G R  L    +++L +  PP +EQ  I  ++    + ID  ++ ++Q +   ++ +
Sbjct: 368 STGDGGRGGLNLTIIRKLHLAFPPKEEQTAIAAIL----SDIDEDIQTLQQRLNKTRQLK 423

Query: 408 SSFIAAAVTGQIDL 421
              +   +TG+I L
Sbjct: 424 QGMMQELLTGKIRL 437


>gi|330937290|gb|EGH41301.1| restriction modification system DNA specificity domain protein
           [Pseudomonas syringae pv. pisi str. 1704B]
          Length = 381

 Score = 77.0 bits (188), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 54/170 (31%), Positives = 76/170 (44%), Gaps = 17/170 (10%)

Query: 8   PQYKDSGV----------QWIGAIPKHWKVVPIKRFTKLNTGRT--SESGKDIIYIGLED 55
           P Y D+G             +G +PK WK   +    +  T +   SE    + Y+GLE 
Sbjct: 156 PSYIDTGTADLFPNDFESSAVGQVPKGWKFGILGDIAQTVTRKATVSEFNDQLNYVGLEH 215

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           +   +   +  +        S+ S+F+K  IL+GKL PY  K +IA  DG+CST  LV Q
Sbjct: 216 IPRKSLSLI--NWGCADGLASSKSVFSKTDILFGKLRPYFHKVVIAPIDGVCSTDVLVCQ 273

Query: 116 PK--DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           PK  D    +L   L S  +      +  GA M    WK +   PM IPP
Sbjct: 274 PKVNDYYGIVLMH-LFSESLISYANRLSNGAKMPRVSWKDLAAYPMCIPP 322


>gi|331017720|gb|EGH97776.1| restriction modification system DNA specificity domain protein
           [Pseudomonas syringae pv. lachrymans str. M302278PT]
          Length = 381

 Score = 76.6 bits (187), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 54/170 (31%), Positives = 76/170 (44%), Gaps = 17/170 (10%)

Query: 8   PQYKDSGV----------QWIGAIPKHWKVVPIKRFTKLNTGRT--SESGKDIIYIGLED 55
           P Y D+G             +G +PK WK   +    +  T +   SE    + Y+GLE 
Sbjct: 156 PSYIDTGTADLFPNDFESSALGQVPKGWKFGILGDIAQTVTRKATVSEFNDQLNYVGLEH 215

Query: 56  VESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
           +   +   +  +        S+ S+F+K  IL+GKL PY  K +IA  DG+CST  LV Q
Sbjct: 216 IPRKSLSLI--NWGCADGLASSKSVFSKTDILFGKLRPYFHKVVIAPIDGVCSTDVLVCQ 273

Query: 116 PK--DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           PK  D    +L   L S  +      +  GA M    WK +   PM IPP
Sbjct: 274 PKVNDYYGIVLMH-LFSESLISYANRLSNGAKMPRVSWKDLAAYPMCIPP 322


>gi|146295063|ref|YP_001185487.1| restriction modification system DNA specificity subunit [Shewanella
           putrefaciens CN-32]
 gi|145566753|gb|ABP77688.1| restriction modification system DNA specificity domain [Shewanella
           putrefaciens CN-32]
          Length = 401

 Score = 76.3 bits (186), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 45/132 (34%), Positives = 72/132 (54%), Gaps = 15/132 (11%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           YIGLE ++SG+ K + + G   + + S   +F KG IL+GK  PYL+KA IA+FDGICS 
Sbjct: 31  YIGLEHLDSGSLK-IKRWGMIAEDNPSFTRVFKKGHILFGKRRPYLKKAAIAEFDGICSG 89

Query: 110 QFLVLQP----KDVLPELLQG---WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
             +V++P    KD+ P ++Q    W  S+  +        G+      +K + N  + IP
Sbjct: 90  DIIVMKPDPDVKDLFPFIVQSKDFWEWSVQTSS-------GSLSPRTKFKSLANFELAIP 142

Query: 163 PLAEQVLIREKI 174
               + L+ E++
Sbjct: 143 DFNRRKLLLEEV 154



 Score = 37.0 bits (84), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 7/85 (8%)

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
           + PK +LPE L  + LS    +    + +  TM+      I N P+P+P + +Q    E+
Sbjct: 309 VDPKIILPEYLYIYALSPWARKYFLCVGQTTTMTTISQSEIENFPVPVPSIYKQ----EE 364

Query: 174 IIAETVRIDTL---ITERIRFIELL 195
           I+     + TL     E I+F+ LL
Sbjct: 365 IVTTFSNLFTLRNRFAEHIKFVSLL 389


>gi|193212616|ref|YP_001998569.1| restriction modification system DNA specificity domain
           [Chlorobaculum parvum NCIB 8327]
 gi|193086093|gb|ACF11369.1| restriction modification system DNA specificity domain
           [Chlorobaculum parvum NCIB 8327]
          Length = 578

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 95/208 (45%), Gaps = 15/208 (7%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK----DIIYIGLEDV 56
           +K+ KA P      V +   +P  W+ V +   T  N GR + SG     D   + LED+
Sbjct: 76  IKNPKALPPITADDVPY--ELPDGWEWVRLGEITAYN-GRKNISGDQIDPDTWVLDLEDI 132

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
           E  T + L +   S +   ST S F KG +LYGKL PYL K ++AD DG+C+T+ + +  
Sbjct: 133 EKDTSRILYRAKFSERQSKSTKSTFLKGDVLYGKLRPYLDKIVVADRDGVCTTEIVPIVS 192

Query: 117 KDVLPELLQGWLLSIDV-TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
              L      WLL        + ++  G  M             P+PPL EQ     +I+
Sbjct: 193 FVGLHSDFLKWLLKRPAFLSYVNSLMYGVKMPRLGTDNAVASIHPLPPLPEQ----HRIV 248

Query: 176 AETVRIDTLITERIRFIELLKEKKQALV 203
           A   RID L+       +L  E++Q  V
Sbjct: 249 A---RIDELMAHCDELEKLRAEREQKRV 273


>gi|259048036|ref|ZP_05738437.1| conserved hypothetical protein [Granulicatella adiacens ATCC 49175]
 gi|259035326|gb|EEW36581.1| conserved hypothetical protein [Granulicatella adiacens ATCC 49175]
          Length = 459

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 95/453 (20%), Positives = 194/453 (42%), Gaps = 61/453 (13%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGKYLP 65
           Y +Y +S + W  +IP+HW V  I +  ++   + S    K+I+ +  +   S       
Sbjct: 4   YEKYSNSEITWSESIPEHWDVKRIAKVFEIRKEKNSPIKTKEILSLSAKYGVSLYTDKKE 63

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL---QPKDVLPE 122
           K GN  + D ++ ++   G IL   +        I+++ G  S  +  L     ++    
Sbjct: 64  KGGNKPKEDLTSYNLCYPGDILVNCMNIVAGSVGISNYLGAVSPVYYPLVNISQENNNTR 123

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHAD------------WKGIGNIPMPIPPLAEQVLI 170
            ++    + +  + +  + +G  MS  D            W  +    +PIPP+ EQ   
Sbjct: 124 YMEYVFRNYNFQRSLVGLGKGIQMSETDAGRLNTVRMRISWDILKTQLLPIPPINEQ--- 180

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKG-----LNPDVKMKDSGIEWV 225
             K IA    +D  I E  R IE+ KEK + +  YI++        N D K      EW+
Sbjct: 181 --KQIANY--LDWKINEIDRLIEINKEKIKCIRKYIISSHEKLILQNSDFK------EWI 230

Query: 226 ------GLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPES 279
                      +++++   +++ ++  +N  L +S+I+  S          + +GL  + 
Sbjct: 231 VKDNIYNFKNKNFKIRKLKSILVKI--ENDALPDSDIIICSNSGKSFVRGDKKIGLYSDD 288

Query: 280 YETYQIVDPGEIVFRFIDLQN-----DKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLA 334
              YQ V+ G+I+   +D  +      K S R ++V+           V     D  Y+ 
Sbjct: 289 INMYQNVNYGQIMIHGMDTWHGAICISKYSGRCSRVVH----------VCETSEDKMYVY 338

Query: 335 WLMRSYDLCKVFYAMGSGLRQSLK----FEDVKRLPVLVPPIKEQFDITNVINVETARID 390
           + +R     K++    +G+RQ+      ++ + ++ +++P I++Q  I + +       +
Sbjct: 339 YYLRLLAFLKMYKPFSNGVRQNTSDFRSWDRLGQVNIILPAIEQQHKIADKLTKLINNSE 398

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            ++++I + I +L   + S I+  VTG+ID+R 
Sbjct: 399 KMIDEIMKEIDMLGNLKQSLISEVVTGKIDVRN 431



 Score = 56.6 bits (135), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/214 (22%), Positives = 97/214 (45%), Gaps = 23/214 (10%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS--YGNIIQKL 268
           +N   K  +S I W   +P+HW+VK    +      KN+ +    ILSLS  YG  +   
Sbjct: 1   MNRYEKYSNSEITWSESIPEHWDVKRIAKVFEIRKEKNSPIKTKEILSLSAKYGVSLYTD 60

Query: 269 ETRNMGLKP-ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY---MAVK 324
           +    G KP E   +Y +  PG+I+   +++      + +      G ++  Y   + + 
Sbjct: 61  KKEKGGNKPKEDLTSYNLCYPGDILVNCMNIVAGSVGISNY----LGAVSPVYYPLVNIS 116

Query: 325 PHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQS-------------LKFEDVKRLPVLVPP 371
               ++ Y+ ++ R+Y+  +    +G G++ S             + ++ +K   + +PP
Sbjct: 117 QENNNTRYMEYVFRNYNFQRSLVGLGKGIQMSETDAGRLNTVRMRISWDILKTQLLPIPP 176

Query: 372 IKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
           I EQ  I N ++ +   ID L+E  ++ I  +++
Sbjct: 177 INEQKQIANYLDWKINEIDRLIEINKEKIKCIRK 210


>gi|89075001|ref|ZP_01161446.1| Restriction modification system DNA specificity domain protein
           [Photobacterium sp. SKA34]
 gi|89049240|gb|EAR54804.1| Restriction modification system DNA specificity domain protein
           [Photobacterium sp. SKA34]
          Length = 402

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 86/406 (21%), Positives = 171/406 (42%), Gaps = 24/406 (5%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTS---ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           +P  W      + TK+  G+     E    + +IG E+V S TG+       S     S 
Sbjct: 2   VPNGWVKTTFGKITKIGNGQVDPKVEPYSSMTHIGPENVVSNTGQITKLKSCSALGLISG 61

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP-ELLQGWLLSIDVTQR 136
              F +  I+Y K+ P L K    DF G+CS     +  +D L    L  ++L     + 
Sbjct: 62  KYEFDENSIVYSKIRPNLNKVCRPDFKGVCSADMYPIWSEDNLDINYLYHYMLGPYFNRI 121

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLK 196
             A+     M   +   + ++ + +PPL EQ     KI       D  I    + I+  K
Sbjct: 122 AIAMSMRTGMPKINRSDLNSLSIVLPPLPEQ----RKIAKILSTWDRGIASTEKLIDASK 177

Query: 197 EKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNI 256
           ++K+AL+  ++T       K +    E      ++WE     +L+ E   +N     + +
Sbjct: 178 QQKKALMQQLLTG------KKRLVDPETGKAFEENWERTHLKSLLIEEKSRNKDNKITRV 231

Query: 257 LSLS-YGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGI 315
           LS++ +   +   +  +  +  E+   Y+IV  G+  F +   + +  S         G+
Sbjct: 232 LSVTNHSGFVLPEDQFSKRVASENISNYKIVKQGQ--FGYNPSRLNVGSFACLNQFSEGV 289

Query: 316 ITSAYM--AVKPHGIDSTYLAWLMRSYDL-CKVFYAMGSGLRQSLKFEDVKRLPVLVPPI 372
           ++  Y+  +     +   YL++ M S++   ++  +    +R+S+ F+ +   P ++P +
Sbjct: 290 LSPMYVVFSTNDSKLQRDYLSYWMDSHEAKQRIKNSTQGSVRESVGFDALCNFPFILPAL 349

Query: 373 KEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
            EQ  I +V+      I++L    E  +  LK+ + + +   +TG+
Sbjct: 350 NEQQKIASVLTAADKEIELL----EAKLAHLKQEKKALMQQLLTGK 391


>gi|293400126|ref|ZP_06644272.1| type I restriction-modification system, specificity subunit
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291306526|gb|EFE47769.1| type I restriction-modification system, specificity subunit
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 204

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 86/172 (50%), Gaps = 10/172 (5%)

Query: 43  ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIAD 102
           +SG +   I LE +E GTG+ L    ++ QS   T +    G +L+GKL PYLRK   A+
Sbjct: 28  DSGVEYPCIELEHIEQGTGRLLGNVSSTTQSSIKTAA--RSGDVLFGKLRPYLRKFAFAE 85

Query: 103 FDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPI 161
            D +CS++     P + V+P+ L  +L+  +   R+  I  G  M  A+W  I   P  I
Sbjct: 86  QDIVCSSEIWAFIPSEYVIPKYLY-YLVQTEHFLRVANISSGTKMPRAEWANIEKEPFDI 144

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVS--YIVTKGL 211
           P     +LI+EKI++    ID  I      + +L   ++ L+   +I   GL
Sbjct: 145 PC----ILIQEKIVSILEAIDKKICTSGDSLRMLINFREGLLQQLFIALSGL 192


>gi|310780627|ref|YP_003968958.1| restriction modification system DNA specificity domain protein
           [Ilyobacter polytropus DSM 2926]
 gi|309749950|gb|ADO84610.1| restriction modification system DNA specificity domain protein
           [Ilyobacter polytropus DSM 2926]
          Length = 392

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 55/153 (35%), Positives = 78/153 (50%), Gaps = 7/153 (4%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
           I LE++   TGK L    +S+Q   S  + F KG ILYGKL PYL+K   ADFDG+CS++
Sbjct: 242 IELENLSQETGKLLGYFNSSQQQ--SIKNKFNKGDILYGKLRPYLKKYYKADFDGVCSSE 299

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
            LVL+ K +    L   + +      I  +  G+ M  ADW+ +  I    P + EQ   
Sbjct: 300 ILVLKGKKLDNNFLYQLIKTFKFNS-IANVSSGSKMPRADWEYMKEILFKYPSILEQ--- 355

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALV 203
            +KI      ID  I    +  E +KE K+ L+
Sbjct: 356 -QKIANFLSGIDKKIELVEQETEQVKEFKRGLL 387


>gi|187779696|ref|ZP_02996169.1| hypothetical protein CLOSPO_03292 [Clostridium sporogenes ATCC
           15579]
 gi|187773321|gb|EDU37123.1| hypothetical protein CLOSPO_03292 [Clostridium sporogenes ATCC
           15579]
          Length = 459

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 111/220 (50%), Gaps = 8/220 (3%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQK 267
           L P    K + + W+  +P HW +   K    +  E+  +N    +  +LSL+   II +
Sbjct: 12  LRPYEDYKKTELLWLDYIPKHWNMIRNKNVMKVEKEIVGRNHS--KYTLLSLTKRGIIPR 69

Query: 268 LETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG 327
                 G  P+ +E YQ+V+P  IVF   D+    R++  + +  +G+IT +Y   K   
Sbjct: 70  DLENAKGKFPKDFEAYQVVNPNNIVFCLFDMDETPRTVGLSSM--KGMITGSYNVFKIEN 127

Query: 328 IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETA 387
           I+  YL +   S D  K   ++ +GLR+ +  E   R  +  PP++EQ  I   ++ + +
Sbjct: 128 INEKYLYYYYLSLDNSKKLRSLYTGLRKVIHIETFLRTKMPNPPMEEQKQIVKYLDCKLS 187

Query: 388 RIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL-RGESQ 426
           +I   +++ ++ I LLK+++  FI  A+ G+I +  GE +
Sbjct: 188 KIRKFIKEKKKIIDLLKQQKKVFINEAIIGKIKIENGECK 227



 Score = 54.3 bits (129), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 58/245 (23%), Positives = 113/245 (46%), Gaps = 25/245 (10%)

Query: 5   KAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGL-------EDVE 57
           + Y  YK + + W+  IPKHW ++  K   K+       +      + L        D+E
Sbjct: 13  RPYEDYKKTELLWLDYIPKHWNMIRNKNVMKVEKEIVGRNHSKYTLLSLTKRGIIPRDLE 72

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
           +  GK+ PKD  + Q       +F     L+  +    R   ++   G+ +  + V + +
Sbjct: 73  NAKGKF-PKDFEAYQVVNPNNIVFC----LFD-MDETPRTVGLSSMKGMITGSYNVFKIE 126

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEG-ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
           ++  + L  + LS+D ++++ ++  G   + H +        MP PP+ EQ  I + +  
Sbjct: 127 NINEKYLYYYYLSLDNSKKLRSLYTGLRKVIHIE--TFLRTKMPNPPMEEQKQIVKYLDC 184

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGL---NPDVK------MKDSGIEWVGL 227
           +  +I   I E+ + I+LLK++K+  ++  +   +   N + K      MK SGI+WV  
Sbjct: 185 KLSKIRKFIKEKKKIIDLLKQQKKVFINEAIIGKIKIENGECKVRYKSEMKPSGIQWVEE 244

Query: 228 VPDHW 232
           +P+HW
Sbjct: 245 IPNHW 249


>gi|228475536|ref|ZP_04060254.1| restriction modification system DNA specificity domain protein
           [Staphylococcus hominis SK119]
 gi|228270318|gb|EEK11753.1| restriction modification system DNA specificity domain protein
           [Staphylococcus hominis SK119]
          Length = 171

 Score = 74.7 bits (182), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 50/172 (29%), Positives = 93/172 (54%), Gaps = 14/172 (8%)

Query: 216 KMKDSGIEWVGLVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRN 272
           +MK+SGI+W+G +P +W+V   K  F     + ++N K  +   LSL+   +I++ +  +
Sbjct: 4   EMKNSGIDWIGEIPKNWKVIKTKHAFKSKKNIVKENAKKYDR--LSLTMNGVIKRDKEDS 61

Query: 273 MGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA-VKPHGIDST 331
            GL+PE +ETYQI+   E++F+ IDL+N    + +++    GI++  Y+  + P   D T
Sbjct: 62  HGLQPEHFETYQIIYKDELIFKLIDLEN----ISTSRGNYTGIVSPVYIRLINP---DET 114

Query: 332 YLAWLMRSYDLCK-VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVI 382
              +       C+ +F  + SG+R SL   ++  +  L  P  E+  I  ++
Sbjct: 115 KYGYYYFYNMWCQHIFNFLSSGVRSSLTANNLLNVSYLKIPFDEKEKIIKIL 166



 Score = 37.0 bits (84), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 21/36 (58%)

Query: 11 KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK 46
          K+SG+ WIG IPK+WKV+  K   K       E+ K
Sbjct: 6  KNSGIDWIGEIPKNWKVIKTKHAFKSKKNIVKENAK 41


>gi|139438849|ref|ZP_01772309.1| Hypothetical protein COLAER_01313 [Collinsella aerofaciens ATCC
           25986]
 gi|133775560|gb|EBA39380.1| Hypothetical protein COLAER_01313 [Collinsella aerofaciens ATCC
           25986]
          Length = 493

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 47/129 (36%), Positives = 67/129 (51%), Gaps = 1/129 (0%)

Query: 46  KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG 105
           +D  +I  ++++ GTGK L           S   +F+ GQILY K+ P LRKA+IA FDG
Sbjct: 76  QDFPHIAPDNIQKGTGKLLFCHSVKADEVKSANHLFSAGQILYSKIRPALRKAVIAPFDG 135

Query: 106 ICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLA 165
           +CS     L  K + PE +   LLS   T+          M   + K +  I +P+PPLA
Sbjct: 136 LCSADMYPLNTK-LQPEYVLTVLLSNFFTEETLKGDTRVKMPKTNQKSLNVILVPVPPLA 194

Query: 166 EQVLIREKI 174
           EQ  I E++
Sbjct: 195 EQRRIVERV 203


>gi|254517360|ref|ZP_05129417.1| restriction modification system DNA specificity domain protein
           [gamma proteobacterium NOR5-3]
 gi|219674198|gb|EED30567.1| restriction modification system DNA specificity domain protein
           [gamma proteobacterium NOR5-3]
          Length = 570

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 83/170 (48%), Gaps = 11/170 (6%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSES---GKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           +P  W+ + +   T       ++    G D   + LEDVE GT + L K     +   S+
Sbjct: 102 LPLSWQWIALGSCTNYGYSDKTDGTDLGPDTWVLELEDVEKGTSRLLQKVRFEDRPFQSS 161

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELLQGWLLSIDVTQR 136
            S+F  G ++YGKL PYL K I+AD  G+C+T+ + ++    + P  L+ +L S    Q 
Sbjct: 162 KSMFEAGDVIYGKLRPYLDKVIVADEGGVCTTEMIPVRGHFGIDPRYLRLFLKSPHFVQY 221

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
             +   G  +           P P+PPLAEQ    ++I+A   ++D L+T
Sbjct: 222 ASSSVHGMNLPRLGTPKAREAPFPLPPLAEQ----KRIVA---KVDELMT 264


>gi|10956235|ref|NP_062461.1| hypothetical protein pCI305_p3 [Lactococcus lactis subsp. lactis]
 gi|9294803|gb|AAF86681.1| HsdS [Lactococcus lactis subsp. lactis]
          Length = 402

 Score = 73.6 bits (179), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 48/162 (29%), Positives = 84/162 (51%), Gaps = 6/162 (3%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           S +  ++  +  ED+ SG G+ L KD + +  D   + +F+   ILYGKL PYL+  ++A
Sbjct: 242 SSNNSELPRVEFEDIVSGEGR-LNKDVSHKFDDRKGI-LFSSQNILYGKLRPYLKNWLLA 299

Query: 102 DFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPI 161
           DF GI    F V +  +  P+ +   L+  +  Q++     G  M  +DWK + +    I
Sbjct: 300 DFKGIALGDFWVFKSINSDPKFVYS-LIQSNHYQKVANDTSGTKMPRSDWKKVSSTEFQI 358

Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALV 203
           P   E+   ++KI +   ++D  I    R ++LLKE+K+  +
Sbjct: 359 PSSLEE---QKKIGSFFKKLDDTIALHQRKLDLLKEQKKGFL 397


>gi|37680389|ref|NP_934998.1| type I restriction-modification system, endonuclease S subunit
           [Vibrio vulnificus YJ016]
 gi|37199136|dbj|BAC94969.1| type I restriction-modification system, endonuclease S subunit
           [Vibrio vulnificus YJ016]
          Length = 389

 Score = 72.8 bits (177), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 84/170 (49%), Gaps = 17/170 (10%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDI-IYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           +P+ W++V      K  + R   S  ++ +Y+GLE ++  + K        R    S V+
Sbjct: 6   LPEGWQMVKFGDIAKHISKRVEPSETELEVYVGLEHLDPDSLKI------KRHGVPSDVA 59

Query: 80  ----IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ--PKDVLPELLQGWLLSIDV 133
               +  KGQI++GK   Y RK  +AD+D ICS   +VL+  PK VLPE L  ++ S   
Sbjct: 60  GQKLLVKKGQIIFGKRRAYQRKVAVADWDCICSAHAMVLEANPKTVLPEFLPVFMQSGYF 119

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDT 183
            +R  AI EG+      WK +      +PPL     ++ K+IA   +I+ 
Sbjct: 120 MERAIAISEGSLSPTIKWKVLEQQKFSLPPLE----LQSKLIARLSKIEN 165


>gi|237741778|ref|ZP_04572259.1| type I restriction-modification system specificity subunit
           [Fusobacterium sp. 4_1_13]
 gi|256845106|ref|ZP_05550564.1| type I restriction-modification system specificity subunit
           [Fusobacterium sp. 3_1_36A2]
 gi|294785606|ref|ZP_06750894.1| conserved hypothetical protein [Fusobacterium sp. 3_1_27]
 gi|229429426|gb|EEO39638.1| type I restriction-modification system specificity subunit
           [Fusobacterium sp. 4_1_13]
 gi|256718665|gb|EEU32220.1| type I restriction-modification system specificity subunit
           [Fusobacterium sp. 3_1_36A2]
 gi|294487320|gb|EFG34682.1| conserved hypothetical protein [Fusobacterium sp. 3_1_27]
          Length = 447

 Score = 72.8 bits (177), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 107/460 (23%), Positives = 193/460 (41%), Gaps = 78/460 (16%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY---------- 50
           M +Y+AY   K + + W+G IP HW++  +KRF  +         KDI Y          
Sbjct: 1   MNNYEAY---KKTDIPWLGKIPSHWEIKRVKRFFYI--------FKDISYKKNPVVLSLA 49

Query: 51  ---IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYL-RKAIIADFDGI 106
              + + D+ES  G+ L ++ N+  S         KG +L   +  Y      I+++DG+
Sbjct: 50  RDKVKIRDIESNKGQ-LAENYNNYNS-------VKKGDLLLNPMDLYSGANCNISNYDGV 101

Query: 107 CSTQFLVLQPKDVLPELLQGWLLSIDVTQ-RIEAICEGATMSHADW----KGIGNIPMPI 161
            S  ++ L+    +      ++  +  T    +++ +G +  +  W    + + N  +PI
Sbjct: 102 ISPAYINLRSNKDISVNFFDYIFKLQYTSLAFQSVGKGVS-KYNRWTLSNETLLNYQLPI 160

Query: 162 PPLAEQVLIREKIIAETVRIDTLI---TERIRFIELLKEKK-QALVSYIVTKGLNPDVKM 217
           PP++EQ+ I   +  +   ID LI    E+I+ +E LK+K    L+S I ++   P    
Sbjct: 161 PPISEQIQIANYLDWKINEIDKLILIEKEQIKELENLKQKYIDKLISSISSE-FKP---- 215

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQK----LETRNM 273
                           +K  F     L+     L E+ +  +SYG I  K      + N+
Sbjct: 216 ----------------LKSIFEFGKGLSITKENLGENGVRCISYGEIHNKFIFSFSSTNL 259

Query: 274 GLKP-ESYETYQIVDPGEIV---FRFIDLQNDKRSLRSAQVMERGI--ITSAYMAVKPHG 327
            LK  E  E   I    E+    F F D   D +   +   +E  +  + + Y  V    
Sbjct: 260 NLKGLEKTEGITISKFAELKKNDFIFADTSEDLKGCGNFTFLEDDVKRVYAGYHTVVAKP 319

Query: 328 I---DSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
           I   +  Y+A+ + S    K       G++  S+    +K   + +P I  Q  ++  I+
Sbjct: 320 ILTFNPRYVAYYLESNKWRKQIRMEVKGIKVYSITQAILKSSRLQLPEIDIQESVSKKID 379

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
                 + L+  +++ I  L+  + S IA  VTG+ID+R 
Sbjct: 380 AFVQYKNALISIMDEKISNLQALKQSLIAEVVTGKIDVRN 419


>gi|260664492|ref|ZP_05865344.1| conserved hypothetical protein [Lactobacillus jensenii SJ-7A-US]
 gi|260561557|gb|EEX27529.1| conserved hypothetical protein [Lactobacillus jensenii SJ-7A-US]
          Length = 376

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 87/362 (24%), Positives = 169/362 (46%), Gaps = 35/362 (9%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG 84
           WK      F+   T  ++    D   I  E++ SG GK       S+ +   +   F KG
Sbjct: 14  WKNKKFLTFSSKITKNSTSDDIDFPRIEFENIVSGEGKL--AQNRSKLNHIKSGIKFDKG 71

Query: 85  QILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGA 144
            IL+GKL PYL+   +A+F G+    F V++ KD        +L+   + +++     G 
Sbjct: 72  DILFGKLRPYLKNWWLAEFPGVAVGDFWVIRAKD--NRYFLYYLIQAPLFEKVSNYTTGT 129

Query: 145 TMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVS 204
            M  +DW  + N    +P + EQ    EKI     ++D+L++        L+++K  L+S
Sbjct: 130 KMPRSDWNYVSNTFFKLPKIDEQ----EKIGRILDKVDSLLS--------LQQRKLELIS 177

Query: 205 YIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKL-IESNILSLSYGN 263
             + KGL   +K +++       + +  E+ P   +   +  KN  L ++ N+  ++ G 
Sbjct: 178 -ALEKGLGQIIKQQNNKYGITFSLNNFLEIPP--QIQARIKNKNQLLTVKLNLQGIARG- 233

Query: 264 IIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM-A 322
            +Q+ +T ++G        Y I   GE++F   ++ N   +L + +    G+ TS  + +
Sbjct: 234 -VQR-DTLSLG-----STKYFIRHTGELIFGKQNIFNGSIALITKEF--DGLATSNDVPS 284

Query: 323 VKPHGIDSTYLAWLMRSYDLCKV--FYAMGSGLRQSLKFEDVKRLPV-LVPPIKEQFDIT 379
           +K   I+  +L +L+++ D  K     A G+G ++ +   D+ +L + ++P  K Q  I 
Sbjct: 285 LKISNINPQFLFYLLKNPDFWKHTELIATGTGSKR-VHIHDLLKLHIKIIPDAKYQAKIV 343

Query: 380 NV 381
           ++
Sbjct: 344 SL 345


>gi|291004532|ref|ZP_06562505.1| restriction modification system DNA specificity domain-containing
           protein [Saccharopolyspora erythraea NRRL 2338]
          Length = 283

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 72/276 (26%), Positives = 122/276 (44%), Gaps = 15/276 (5%)

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVK 216
           +P P   L EQ  I + + AET RID L   R R +++L+EK    V Y   +G      
Sbjct: 2   LPFPRVSLEEQRRIADFLDAETTRIDKLSALRERQLDILEEKAMRRV-YDTVRGTGVVGA 60

Query: 217 MKDSGIEWVGLVPDHWEVKP---FFA------LVTELNRKNTKLIESNILSLSYGNIIQK 267
            + SG+ W+G VP HW V     +F       L  E  R +       + ++ +G ++  
Sbjct: 61  RRPSGLSWLGSVPVHWRVAAVSHYFEVELGKMLNQERARGDHLRPYLRVANVQWG-VVDT 119

Query: 268 LETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG 327
            E   M   PE  + Y++  PG+++         + ++ S ++ E      A   ++P G
Sbjct: 120 TELAMMDFPPEEQKRYRL-QPGDLLVNEGGSWPGRAAVWSGEI-EEIYYQKALHRIRPRG 177

Query: 328 IDST-YLAWLMRSYDLCKVFYAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVE 385
           ++ST +L + + + +  KVF   G S     L  E ++      P + EQ      +   
Sbjct: 178 MESTWWLYFCLVAAERMKVFQVQGNSSTMTHLTREQLRPQRFPFPDLAEQEQAVERLKDA 237

Query: 386 TARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            A+   +   + +    L ERR + I AAVTG+ D+
Sbjct: 238 EAKDRQIRRVLSRQQATLAERRQALITAAVTGEFDV 273


>gi|23452777|gb|AAN33159.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452791|gb|AAN33167.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
          Length = 403

 Score = 72.0 bits (175), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 88/172 (51%), Gaps = 13/172 (7%)

Query: 37  NTGRTSE------SGKDIIYIGLEDVESGTGKYLPKD-GNSRQSDTSTVSIFAKGQILYG 89
           N G+TS+       G D I + LED+E  +G  L K     RQS ++ +  F KG IL+G
Sbjct: 223 NYGKTSQVKPSQLKGNDWI-LELEDIEKESGVLLQKVLFQDRQSKSNKIK-FNKGDILFG 280

Query: 90  KLGPYLRKAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSH 148
            L PYL+K IIAD +G CS++ +     + +    +  +L +  +  RI ++  GA M  
Sbjct: 281 TLRPYLKKVIIADDNGACSSEIMPFSTGNSITNHFIYYYLFANFLHDRISSLTYGARMPR 340

Query: 149 ADWKGIGNIPMPIPPLAEQVLIREK---IIAETVRIDTLITERIRFIELLKE 197
              K   ++ +P+PPL EQ  I E    +  +   +  L T+ ++  E LK+
Sbjct: 341 LGTKDGKSLQIPLPPLQEQEQIAEHLDFVFEKAKALKELYTKELKDYEELKQ 392


>gi|332292954|ref|YP_004431563.1| restriction modification system DNA specificity domain protein
           [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171040|gb|AEE20295.1| restriction modification system DNA specificity domain protein
           [Krokinobacter diaphorus 4H-3-7-5]
          Length = 413

 Score = 72.0 bits (175), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 44/131 (33%), Positives = 70/131 (53%), Gaps = 5/131 (3%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAI 140
           F+KG+IL+GKL P L+K IIA FDG+CS++  VL  K++  E L   L+  +       +
Sbjct: 91  FSKGEILFGKLRPNLKKYIIAPFDGVCSSEIWVLNGKELSNEFL-FRLIQTNKFHSSTLV 149

Query: 141 CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQ 200
             G+ M  ADW  I +   P P L EQ    +KI +    +D  I +  +   LL++ K+
Sbjct: 150 TSGSKMPRADWAYISSSIFPFPSLPEQ----QKIASFLSAVDKKIQQLTKKKALLEQYKK 205

Query: 201 ALVSYIVTKGL 211
            ++  + +  L
Sbjct: 206 GVMQQLFSGQL 216


>gi|23452718|gb|AAN33132.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
          Length = 403

 Score = 72.0 bits (175), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 88/172 (51%), Gaps = 13/172 (7%)

Query: 37  NTGRTSE------SGKDIIYIGLEDVESGTGKYLPKD-GNSRQSDTSTVSIFAKGQILYG 89
           N G+TS+       G D I + LED+E  +G  L K     RQS ++ +  F KG IL+G
Sbjct: 223 NYGKTSQVKPSQLKGNDWI-LELEDIEKESGVLLQKVLFQDRQSKSNKIK-FNKGDILFG 280

Query: 90  KLGPYLRKAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSH 148
            L PYL+K IIAD +G CS++ +     + +    +  +L +  +  RI ++  GA M  
Sbjct: 281 TLRPYLKKVIIADDNGACSSEIMPFSTGNSITNHFIYYYLFANFLHDRISSLTYGARMPR 340

Query: 149 ADWKGIGNIPMPIPPLAEQVLIREK---IIAETVRIDTLITERIRFIELLKE 197
              K   ++ +P+PPL EQ  I E    +  +   +  L T+ ++  E LK+
Sbjct: 341 LGTKDGKSLQIPLPPLQEQEQIAEHLDFVFEKAKALKELYTKELKDYEELKQ 392


>gi|148925704|ref|ZP_01809392.1| putative type I specificity subunit HsdS [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|157415770|ref|YP_001483026.1| hypothetical protein C8J_1451 [Campylobacter jejuni subsp. jejuni
           81116]
 gi|19881216|gb|AAM00830.1|AF486546_4 HsdS [Campylobacter jejuni]
 gi|19881256|gb|AAM00863.1|AF486553_4 HsdS [Campylobacter jejuni]
 gi|19881280|gb|AAM00883.1|AF486557_4 HsdS [Campylobacter jejuni]
 gi|19881299|gb|AAM00895.1|AF486564_1 HsdS [Campylobacter jejuni]
 gi|23452712|gb|AAN33130.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452721|gb|AAN33133.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452731|gb|AAN33137.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452734|gb|AAN33138.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452736|gb|AAN33139.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452751|gb|AAN33145.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452754|gb|AAN33146.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452759|gb|AAN33148.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|23452761|gb|AAN33149.1| putative type I specificity subunit HsdS [Campylobacter jejuni]
 gi|145845714|gb|EDK22805.1| putative type I specificity subunit HsdS [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|157386734|gb|ABV53049.1| hypothetical protein C8J_1451 [Campylobacter jejuni subsp. jejuni
           81116]
 gi|307748412|gb|ADN91682.1| Putative type I specificity subunit HsdS [Campylobacter jejuni
           subsp. jejuni M1]
 gi|315931058|gb|EFV10033.1| type I restriction modification DNA specificity domain protein
           [Campylobacter jejuni subsp. jejuni 327]
          Length = 403

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 88/172 (51%), Gaps = 13/172 (7%)

Query: 37  NTGRTSE------SGKDIIYIGLEDVESGTGKYLPKD-GNSRQSDTSTVSIFAKGQILYG 89
           N G+TS+       G D I + LED+E  +G  L K     RQS ++ +  F KG IL+G
Sbjct: 223 NYGKTSQVKPSQLKGNDWI-LELEDIEKESGVLLQKVLFQDRQSKSNKIK-FNKGDILFG 280

Query: 90  KLGPYLRKAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSH 148
            L PYL+K IIAD +G CS++ +     + +    +  +L +  +  RI ++  GA M  
Sbjct: 281 TLRPYLKKVIIADDNGACSSEIMPFSTGNSITNHFIYYYLFANFLHDRISSLTYGARMPR 340

Query: 149 ADWKGIGNIPMPIPPLAEQVLIREK---IIAETVRIDTLITERIRFIELLKE 197
              K   ++ +P+PPL EQ  I E    +  +   +  L T+ ++  E LK+
Sbjct: 341 LGTKDGKSLQIPLPPLQEQEQIAEHLDFVFEKAKALKELYTKELKDYEELKQ 392


>gi|325917799|ref|ZP_08179981.1| restriction endonuclease S subunit [Xanthomonas vesicatoria ATCC
           35937]
 gi|325535973|gb|EGD07787.1| restriction endonuclease S subunit [Xanthomonas vesicatoria ATCC
           35937]
          Length = 756

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/156 (32%), Positives = 71/156 (45%), Gaps = 2/156 (1%)

Query: 21  IPKHWKVVPIKRFTKLN-TGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           +P  W+   +   T    T +  E  +D   + LED+E  T K L K     ++  S  +
Sbjct: 83  LPVTWEWARLGEITNFGITVKKEEIPEDAWVLDLEDIEKDTSKLLQKARFKERNSLSDKN 142

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWLLSIDVTQRIE 138
            F KG +LYGKL PYL K ++AD DG C+T+ L  +     L     G L S    + + 
Sbjct: 143 FFNKGDVLYGKLRPYLNKVLVADEDGFCTTEILPFRCYGPFLANYFMGALKSPYFLRYVN 202

Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
           A   G  M     +       P+PPLAEQ  I  K+
Sbjct: 203 ARSYGMKMPRLGTEDGRQALFPLPPLAEQYRIVAKV 238



 Score = 62.8 bits (151), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 81/169 (47%), Gaps = 21/169 (12%)

Query: 68  GNSRQSDTSTV---------SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
           G  R +D  TV         S F  GQI+Y K+ P L KA++ DFDG+CS     + P D
Sbjct: 403 GTGRLTDNRTVKDSGVKGPNSRFFAGQIVYSKIRPSLSKAVLVDFDGLCSAD---MYPID 459

Query: 119 VL--PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
                E L   +LS    +++        M   + + + N  +PIPPLAEQ     +I+A
Sbjct: 460 AFINSEFLLKEILSAVFLEQVRVAENRIKMPKLNQESMANFVLPIPPLAEQ----RRIVA 515

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           +  ++  L  +    +  +++   +L + ++ + LN +   K+SG E V
Sbjct: 516 KVDQLMALCDQLKARLGEVRQVHGSLANALIGQALNGE---KESGAEVV 561


>gi|94263943|ref|ZP_01287746.1| Restriction modification system DNA specificity domain [delta
           proteobacterium MLMS-1]
 gi|93455688|gb|EAT05867.1| Restriction modification system DNA specificity domain [delta
           proteobacterium MLMS-1]
          Length = 414

 Score = 71.2 bits (173), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 49/170 (28%), Positives = 78/170 (45%), Gaps = 4/170 (2%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTS---ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSD 74
           IG IPK W+V  I    +  +G+ S       D+  +  + +E  TG+ + ++    Q  
Sbjct: 210 IGRIPKEWEVKNILDLVEFPSGQVSPLVSPYIDMSLVAPDHIERNTGRLMLRETAREQGA 269

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL-PELLQGWLLSIDV 133
            S   +F  G I+Y K+ PYLRKAI+ADFDGICS     L+ K    P  + G +L    
Sbjct: 270 ISGKYVFESGDIVYSKIRPYLRKAILADFDGICSADMYPLKVKQGNDPLFIFGVILGERF 329

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDT 183
           +   E++   +     +          +P   EQ+ I E I +   +I +
Sbjct: 330 STYAESVSMRSGFPKINRSEFSGFSCAVPSNNEQMKISEIIESAEAKIKS 379


>gi|34762432|ref|ZP_00143432.1| TYPE I RESTRICTION-MODIFICATION SYSTEM SPECIFICITY SUBUNIT
           [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
 gi|27887900|gb|EAA24968.1| TYPE I RESTRICTION-MODIFICATION SYSTEM SPECIFICITY SUBUNIT
           [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
          Length = 447

 Score = 70.9 bits (172), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 107/460 (23%), Positives = 192/460 (41%), Gaps = 78/460 (16%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY---------- 50
           M +Y+AY   K + + W+G IP HW++  +KRF  +         KDI Y          
Sbjct: 1   MNNYEAY---KKTDIPWLGKIPSHWEIKRVKRFFYI--------FKDISYKKNPVVLSLA 49

Query: 51  ---IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYL-RKAIIADFDGI 106
              + + D+ES  G+ L ++ N+  S         KG +L   +  Y      I+++DG+
Sbjct: 50  RDKVKIRDIESNKGQ-LAENYNNYNS-------VKKGDLLLNPMDLYSGANCNISNYDGV 101

Query: 107 CSTQFLVLQPKDVLPELLQGWLLSIDVTQ-RIEAICEGATMSHADW----KGIGNIPMPI 161
            S  ++ L+    +      ++  +  T    +++ +G +  +  W    + + N  +PI
Sbjct: 102 ISPAYINLRSNKDISVNFFDYIFKLQYTSLAFQSVGKGVS-KYNRWTLSNETLLNYQLPI 160

Query: 162 PPLAEQVLIREKIIAETVRIDTLI---TERIRFIELLKEKK-QALVSYIVTKGLNPDVKM 217
           PP++EQ+ I   +  +   ID LI    E+I+ +E LK+K    L+S I ++   P    
Sbjct: 161 PPISEQIQIANYLDWKINEIDKLILIEKEQIKELENLKQKYIDKLISSISSE-FKP---- 215

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQK----LETRNM 273
                           +K  F     L+     L E+ +  +SYG I  K      + N 
Sbjct: 216 ----------------LKSIFEFGKGLSITKENLGENGVRCISYGEIHNKFIFSFSSTNP 259

Query: 274 GLKP-ESYETYQIVDPGEIV---FRFIDLQNDKRSLRSAQVMERGI--ITSAYMAVKPHG 327
            LK  E  E   I    E+    F F D   D +   +   +E  +  + + Y  V    
Sbjct: 260 NLKGLEKTEGITISKFAELKKNDFIFADTSEDLKGCGNFTFLEDDVKRVYAGYHTVVAKP 319

Query: 328 I---DSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
           I   +  Y+A+ + S    K       G++  S+    +K   + +P I  Q  ++  I+
Sbjct: 320 ILTFNPRYVAYYLESNKWRKQIRMEVKGIKVYSITQAILKSSRLQLPEIDIQESVSKKID 379

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
                 + L+  +++ I  L+  + S IA  VTG+ID+R 
Sbjct: 380 AFVQYKNALISIMDEKISNLQALKQSLIAEVVTGKIDVRN 419


>gi|332362406|gb|EGJ40206.1| type I restriction-modification system [Streptococcus sanguinis
           SK1056]
          Length = 170

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 54/88 (61%)

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           + +L+ +YD+CKVFY  G G+RQ   + D+ ++ +L+PP  EQ  I + ++ + A++D  
Sbjct: 1   MYYLLHTYDICKVFYNFGGGVRQGGTWSDIYKMELLIPPCNEQQKIADYLDKKIAQLDRA 60

Query: 393 VEKIEQSIVLLKERRSSFIAAAVTGQID 420
              +E+ I  LK+ RSS I   VT  +D
Sbjct: 61  KRLLEKQIQKLKDYRSSLIYETVTKGLD 88



 Score = 59.7 bits (143), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 52/95 (54%), Gaps = 6/95 (6%)

Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIRE---KIIAETVRIDTLITERIRFIELLKEKK 199
           G       W  I  + + IPP  EQ  I +   K IA+  R   L+ ++I   + LK+ +
Sbjct: 19  GGVRQGGTWSDIYKMELLIPPCNEQQKIADYLDKKIAQLDRAKRLLEKQI---QKLKDYR 75

Query: 200 QALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
            +L+   VTKGL+  V MKDSGI+W+G VP+ W V
Sbjct: 76  SSLIYETVTKGLDKTVPMKDSGIDWIGQVPEGWGV 110


>gi|313634897|gb|EFS01303.1| putative type-1 restriction enzyme MjaXIP specificity protein
           [Listeria seeligeri FSL N1-067]
          Length = 439

 Score = 70.5 bits (171), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 44/54 (81%)

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
           ID LI+ + + I+LL+E++QA+++  VTKGLN  V+MKDSG+EW+G +P HWE+
Sbjct: 173 IDFLISSKEKQIKLLEEQRQAMITEAVTKGLNSSVRMKDSGVEWIGEIPKHWEI 226



 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 89/218 (40%), Gaps = 28/218 (12%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVES-GTGKYLPKDGN 69
           KDSGV+WIG IPKHW++  IK +T    GR       I + GL   E    G YL    N
Sbjct: 210 KDSGVEWIGEIPKHWEIAKIK-YTTYVKGR-------IGWQGLRSDEFIDDGPYLVTGTN 261

Query: 70  SRQ-----SDTSTVS----------IFAKGQILYGKLGPYLRKAIIADFDG--ICSTQFL 112
            +       D   +S             +  +L  K G   + A++ +  G  I ++   
Sbjct: 262 FKNGIVDWQDCYHISEDRYNEAVPIQLKEDDLLITKDGTIGKLALVKEMPGKTILNSGIF 321

Query: 113 VLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           V +P     +   L   L S   +Q I  +  G+T+ H   +   N    +P L EQ  I
Sbjct: 322 VTRPLANKYINNYLYWNLNSASFSQYIRTMETGSTIKHLYQETFVNYSYALPSLEEQESI 381

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
              +  +  ++  +I      I  LKE + +L+   VT
Sbjct: 382 SCYLNNKNQKLGNVIQNITIQISKLKEYRHSLIHEAVT 419


>gi|323526111|ref|YP_004228264.1| restriction modification system DNA specificity domain-containing
           protein [Burkholderia sp. CCGE1001]
 gi|323383113|gb|ADX55204.1| restriction modification system DNA specificity domain protein
           [Burkholderia sp. CCGE1001]
          Length = 443

 Score = 70.5 bits (171), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 85/380 (22%), Positives = 160/380 (42%), Gaps = 28/380 (7%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           LED+E    + + +   + +   ST + F+KG +LYGKL PYL K ++AD +G+C+T+ +
Sbjct: 39  LEDIEKDKSRIVSRLTFADRKSKSTKNRFSKGDVLYGKLRPYLNKVVLADSNGLCTTEII 98

Query: 113 -VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
            + Q   V    +  WL           +  G  M         + P  +PPLAEQ  I 
Sbjct: 99  PIKQTAAVDNRYVFHWLRGPRFLSYAIGVSHGLNMPRLGTDAGRSAPFILPPLAEQKRIA 158

Query: 172 EKIIAETVRIDTLITERIRFIELLKE-KKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPD 230
           +K+ +   R++       R   +L   ++ ALV+ ++  G + D K     I +  L+  
Sbjct: 159 DKLDSVLSRVEAACARMGRVPTILTRLRRAALVATLL--GQDGDAK-PTPRIAFGSLIN- 214

Query: 231 HWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
              ++     V + ++    ++ S+  S+  G I    E        +S E    +   +
Sbjct: 215 --SIRGGTTAVPQSDKTAYPILRSS--SVRQGRI--DFEDVRYLTSEQSGEEKNFIREND 268

Query: 291 IVFRFIDLQND---------KRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYD 341
           ++F  ++   +           SL   Q  +R      Y A     I   Y A+     D
Sbjct: 269 VLFTRLNGNVNYVGNCAVVPSVSLNKYQYPDR-----LYCARLKETIVPKYCAYAFALPD 323

Query: 342 LCKVF--YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           + K     A  S   + +  +D+K + + +PP+ EQ  + N I    A  D L + ++++
Sbjct: 324 IRKEIERRAKSSAGHKRISIQDIKEMEIPLPPVAEQLRMVNQIERIFATCDRLEKTLDEA 383

Query: 400 IVLLKERRSSFIAAAVTGQI 419
            ++      + +A A  G++
Sbjct: 384 KIVADHLTPALLAKAFRGEL 403


>gi|159897810|ref|YP_001544057.1| restriction modification system DNA specificity subunit
           [Herpetosiphon aurantiacus ATCC 23779]
 gi|159890849|gb|ABX03929.1| restriction modification system DNA specificity domain
           [Herpetosiphon aurantiacus ATCC 23779]
          Length = 398

 Score = 70.1 bits (170), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 90/201 (44%), Gaps = 12/201 (5%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGK---DIIYIGLEDVESGT----GKYLPKDGNSRQS 73
           IP  W  V +      + G   +      D   + LED+E  T    G++L K+   + +
Sbjct: 75  IPPSWIWVSLDDIVVYDAGSKHDPNNLDPDSWLLELEDIEKNTSVILGQFLVKERKPKSN 134

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELLQGWLLSID 132
             S    F K  ILYGKL PYL K I+A   G C+T+ +VL+PK ++ P  +Q +L S  
Sbjct: 135 KAS----FQKNDILYGKLRPYLNKVIVAHTSGFCTTEIVVLRPKLELSPFYIQNFLKSPF 190

Query: 133 VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFI 192
               +     G  M            +P+PPLAEQ  I  K+       D L  ++    
Sbjct: 191 FVSYVNQHSYGTKMPRLGTLDGKKASIPLPPLAEQQRIVAKVAQLMALCDQLEQQQTSRE 250

Query: 193 ELLKEKKQALVSYIVTKGLNP 213
            L ++ +Q+ +  ++++   P
Sbjct: 251 ALRQQVQQSAIKQLLSELARP 271


>gi|126176529|ref|YP_001052678.1| restriction modification system DNA specificity subunit [Shewanella
           baltica OS155]
 gi|125999734|gb|ABN63809.1| restriction modification system DNA specificity domain [Shewanella
           baltica OS155]
          Length = 363

 Score = 69.7 bits (169), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 62/200 (31%), Positives = 90/200 (45%), Gaps = 16/200 (8%)

Query: 46  KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG 105
           +DI YIGLE V   T + L K G+S   +++    F KG IL+G L PY RK  IA FDG
Sbjct: 23  EDIPYIGLEHVSQQTLQLLGK-GSSLNVESNKYK-FKKGDILFGTLRPYFRKVTIAPFDG 80

Query: 106 ICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLA 165
           +CST++ V++PK         + L+ +                  WK   +  +      
Sbjct: 81  VCSTEYSVIRPKKADYTNFVFYFLANEKFIEYATTNSVGARPRTKWKLFSDYKVRKTRNQ 140

Query: 166 EQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWV 225
           E+  I  K+ A    +D LI    R I+LL+E  + L            V ++  G E V
Sbjct: 141 EKFDIGFKLRA----LDDLIENNRRRIQLLEESARLLYQEWF-------VHLRFPGHELV 189

Query: 226 GL---VPDHWEVKPFFALVT 242
            +   VP+ WE KP   + T
Sbjct: 190 KVIDGVPEGWEKKPIKQIAT 209


>gi|49484938|ref|YP_042159.1| putative type I restriction enzyme specificity protein
           [Staphylococcus aureus subsp. aureus MSSA476]
 gi|49243381|emb|CAG41798.1| putative type I restriction enzyme specificity protein
           [Staphylococcus aureus subsp. aureus MSSA476]
          Length = 436

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 106/237 (44%), Gaps = 17/237 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT--------SESGKDIIYIGLEDVESGTGK 62
           K SG++WIG IPK+W +  +K      +G          S++ K +I      ++S   K
Sbjct: 6   KYSGIEWIGYIPKYWTITKLKNIIDFISGYAFKSELFTISDNNKKVI-----TIKSFNTK 60

Query: 63  YLPKDGNSRQSDT---STVSIFAKGQILYGKLGPYLRKAI-IADFDGICSTQFLVLQPKD 118
            +  D  S  +++    T  +     IL+   G    K + I   D +      V   + 
Sbjct: 61  EIILDNLSYSNESLKFPTKYLLKNNDILFAMSGGTTGKNLLIEQVDDLYYINQRVGIIRS 120

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
              + +  ++ +   ++ I     G+   +     I N  + +P       I   I  + 
Sbjct: 121 SFSKFIYYYINTGLFSEYINLFSSGSAQPNISATDIQNFIIALPEKETIKKIEIYINYQL 180

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
             I  +I    + IE LK+ KQ+L++  VTKG++P+V+MK+SG +W+G +P +W V+
Sbjct: 181 KIISNIIDTTYQSIEELKKYKQSLITEAVTKGIDPNVEMKESGNDWIGSIPSNWSVR 237



 Score = 39.7 bits (91), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 50/223 (22%), Positives = 93/223 (41%), Gaps = 30/223 (13%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGN----IIQKLETR 271
           +MK SGIEW+G +P +W +     ++  ++    K   S + ++S  N     I+   T+
Sbjct: 4   EMKYSGIEWIGYIPKYWTITKLKNIIDFISGYAFK---SELFTISDNNKKVITIKSFNTK 60

Query: 272 NMGLKPESYETYQIVDPGEIVFRFIDL------QNDKRSLRSAQV-------MERGIITS 318
            + L   SY    +  P + + +  D+          ++L   QV          GII S
Sbjct: 61  EIILDNLSYSNESLKFPTKYLLKNNDILFAMSGGTTGKNLLIEQVDDLYYINQRVGIIRS 120

Query: 319 AYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFD 377
           ++         S ++ + + +    +      SG  Q ++   D++   + +P  +    
Sbjct: 121 SF---------SKFIYYYINTGLFSEYINLFSSGSAQPNISATDIQNFIIALPEKETIKK 171

Query: 378 ITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQID 420
           I   IN +   I  +++   QSI  LK+ + S I  AVT  ID
Sbjct: 172 IEIYINYQLKIISNIIDTTYQSIEELKKYKQSLITEAVTKGID 214


>gi|88707236|ref|ZP_01104922.1| type I restriction-modification system, endonuclease S subunit
           [Congregibacter litoralis KT71]
 gi|88698519|gb|EAQ95652.1| type I restriction-modification system, endonuclease S subunit
           [Congregibacter litoralis KT71]
          Length = 398

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 83/369 (22%), Positives = 150/369 (40%), Gaps = 67/369 (18%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE ++  + K + + G + + ++S + +F  G I++GK   Y RK  +ADFDGICS 
Sbjct: 34  YVGLEHIDPESLK-IRRWGETSEVESSKI-LFKSGDIIFGKRRAYQRKLCVADFDGICSA 91

Query: 110 QFLVLQPKD--VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
             +VL+PK   VL + L  ++ S     R   I  G      +W+ +      +PPL EQ
Sbjct: 92  HAMVLRPKTDVVLEDFLPFFMQSEIFMNRAVKISVGGLSPTINWRDLAKEEFALPPLQEQ 151

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I + + A     + L          L E+  +    +V   +        +  E VG 
Sbjct: 152 RRIVQLLSAAERYQNALYD--------LSERGTSSRDSLVDHRMRGATLGATTYHERVGR 203

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIES-------NILSLSYGNIIQKLETRNMGLKPESY 280
             + W + P   L+T      ++ +          +++L  G      + + + L    +
Sbjct: 204 YFNGWNLVPLGELLTAAQYGLSESLHGKGQYPILRMMNLEDGKATAD-DLKYLDLSDSDF 262

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGI-----DSTYLAW 335
           ETY++V  G+++F                       T++Y  V   G+     D  + ++
Sbjct: 263 ETYRLVS-GDVLFN---------------------RTNSYELVGRTGVYDLPGDFVFASY 300

Query: 336 LMR--------SYDLCKVFYAMGSGLRQSLKF------------EDVKRLPVLVPPIKEQ 375
           L+R        S +    F     G RQ + F             ++KR+ V +PPI  Q
Sbjct: 301 LIRLKTDIDRLSPEYLSAFLRAPIGRRQVMSFATRGVSQANINASNLKRVLVPLPPIGYQ 360

Query: 376 FDITNVINV 384
            ++  ++ V
Sbjct: 361 KEVVELLTV 369


>gi|187930240|ref|YP_001900727.1| restriction modification system [Ralstonia pickettii 12J]
 gi|187727130|gb|ACD28295.1| restriction modification system, type I [Ralstonia pickettii 12J]
          Length = 394

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 85/193 (44%), Gaps = 7/193 (3%)

Query: 26  KVVPIKRFTKLNTGRTSESGKDII--YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAK 83
           ++V      +L+  R+ +   D I  Y+GLE +E G  +   +   S     +  S+F  
Sbjct: 11  RLVKFGDVVRLSKARSQDPLADGIERYVGLEHLEPGDLRI--RSWGSVADGVTFTSVFQP 68

Query: 84  GQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSIDVTQRIEAI 140
           GQ+L+GK   Y RK  +ADF G+CS    VL+ KD   +LPELL     +          
Sbjct: 69  GQVLFGKRRAYQRKVAVADFSGVCSGDIYVLETKDAQVLLPELLLFICQTDAFFDHAVGT 128

Query: 141 CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQ 200
             G+     +W  + +    +PP+ EQ      + A T +   +    +    +L+  K 
Sbjct: 129 SAGSLSPRTNWASLADFEFVLPPIEEQQSAIVLLSAATDQCHAIEAAHLAAGRMLQSFKD 188

Query: 201 ALVSYIVTKGLNP 213
           +++ Y  +   NP
Sbjct: 189 SMLLYNTSAVANP 201


>gi|260891564|ref|ZP_05902827.1| hypothetical protein GCWU000323_02779 [Leptotrichia hofstadii
           F0254]
 gi|260858672|gb|EEX73172.1| hypothetical protein GCWU000323_02779 [Leptotrichia hofstadii
           F0254]
          Length = 461

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 85/444 (19%), Positives = 194/444 (43%), Gaps = 44/444 (9%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGKYLP 65
           Y +YK + + W   +P +W +  I     +   + S    K+I+ +  +   S       
Sbjct: 4   YERYKSTELSWSKHLPYYWNIKRIASIFDIRKEKNSPVRTKEILSLSAKYGVSLYSDKKE 63

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQF---LVLQPKDVLPE 122
           K GN  + D ++  +   G IL   +        I+++ G  S  +   L +   +    
Sbjct: 64  KGGNKPKEDLTSYYLCYSGDILVNCMNIVAGSVGISNYFGAVSPVYYPLLNMNADENCTR 123

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHAD------------WKGIGNIPMPIPPLAEQVLI 170
            ++    + +  + +  + +G  MS ++            W  +    +P+PP+ EQV I
Sbjct: 124 YMEYVFRNYNFQRSLVGLGKGIQMSESEDGKLFTVRMRISWDILKTQLLPVPPIEEQVQI 183

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKG----LNPDVKMKDSGIEWVG 226
                     +D  I E  + IE+ KEK + +  YI+++     LN D ++K   IE   
Sbjct: 184 AN-------YLDWKINEINKLIEINKEKIKEIRKYIISEHERLILNNDSEVKKLIIE--N 234

Query: 227 LVPDHWE----VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET 282
            + D+ +    +K   +++ ++ ++ +  ++S+I+  S          + +GL  ++ + 
Sbjct: 235 NIYDYSDKKIKIKRLKSVLKKIEKEAS--LDSDIIICSNNGKSFVRGDKKIGLYSDNIKM 292

Query: 283 YQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDL 342
           YQ ++ G+++   +D  +    +        G  T      + +  D  Y+ + +R    
Sbjct: 293 YQNINKGQLMIHGMDTWHGAICISDYN----GRCTKVVHVCETNE-DKMYIYYYLRLLAF 347

Query: 343 CKVFYAMGSGLRQSLK----FEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
            +++    +G+RQ+      ++ + ++ +++P I++Q++I+N +       + L+ +I  
Sbjct: 348 LEMYKPFSNGVRQNTSDFRSWDKLGQINIIIPLIEKQYEISNTLTEIINNSEKLILEIIN 407

Query: 399 SIVLLKERRSSFIAAAVTGQIDLR 422
              +L + + S I+  VTGQID+R
Sbjct: 408 ESEMLNKLKQSLISEVVTGQIDVR 431



 Score = 46.2 bits (108), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 46/204 (22%), Positives = 87/204 (42%), Gaps = 25/204 (12%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS--YGNIIQKL 268
           +N   + K + + W   +P +W +K   ++      KN+ +    ILSLS  YG  +   
Sbjct: 1   MNKYERYKSTELSWSKHLPYYWNIKRIASIFDIRKEKNSPVRTKEILSLSAKYGVSLYSD 60

Query: 269 ETRNMGLKP-ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG 327
           +    G KP E   +Y +   G+I+   +++      + +      G ++  Y  +    
Sbjct: 61  KKEKGGNKPKEDLTSYYLCYSGDILVNCMNIVAGSVGISNY----FGAVSPVYYPLLNMN 116

Query: 328 IDST---YLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVL--------------VP 370
            D     Y+ ++ R+Y+  +    +G G++ S + ED K   V               VP
Sbjct: 117 ADENCTRYMEYVFRNYNFQRSLVGLGKGIQMS-ESEDGKLFTVRMRISWDILKTQLLPVP 175

Query: 371 PIKEQFDITNVINVETARIDVLVE 394
           PI+EQ  I N ++ +   I+ L+E
Sbjct: 176 PIEEQVQIANYLDWKINEINKLIE 199


>gi|32263453|gb|AAP78481.1| S.AhdI [Aeromonas hydrophila]
          Length = 227

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/170 (31%), Positives = 87/170 (51%), Gaps = 10/170 (5%)

Query: 46  KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIAD--- 102
           + I Y+GLE+V S TG+ +  +  +  S  S   IF  G IL+G+L P L K  + D   
Sbjct: 57  RQISYLGLENVRSQTGELVGFEPRAASSIKSRSKIFGLGDILFGRLRPELNKVYLVDGEP 116

Query: 103 FDGICSTQFLVLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
            +GICS +F+VL P    V    ++  + S  VT+ IE    GA++       +  I +P
Sbjct: 117 SEGICSGEFIVLAPITSRVNARYVRHIIASPFVTKFIEKFRVGASLPRIAADDLLGIKVP 176

Query: 161 IPPLAEQVLIREKIIAETVRIDT-LITERIRFIELLKEKKQALVSYIVTK 209
           +PPL     ++E+I      +D  L   R+R  EL  ++ +AL+  + +K
Sbjct: 177 VPPLE----VQEQIARRLAEMDQELRGLRLRVEELPSQQLEALMMAVGSK 222


>gi|294495711|ref|YP_003542204.1| restriction modification system DNA specificity domain protein
           [Methanohalophilus mahii DSM 5219]
 gi|292666710|gb|ADE36559.1| restriction modification system DNA specificity domain protein
           [Methanohalophilus mahii DSM 5219]
          Length = 414

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 108/226 (47%), Gaps = 25/226 (11%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDII------YIGLEDVESGT---GKYLPKDGNSR 71
           IP  W++V   +F  +  G+ S+  +D        YIG E  + G     K  P  GN  
Sbjct: 5   IPNGWEIV---KFGDV-VGKVSDKFQDRSAWHFERYIGGEHFDEGAIRVTKSNPIKGNED 60

Query: 72  QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLL 129
              ++    F  G +LY    P LRK  + DF+GICS    VLQ  +  +L  LL   + 
Sbjct: 61  VIGSAFHMRFKPGHVLYVSRNPRLRKGGMVDFEGICSNTTYVLQADESKLLQSLLPFIIQ 120

Query: 130 SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV-RIDTLITER 188
           +    +       G+T    +WK I N  + +PP+ EQ     K +AE +  ++  I + 
Sbjct: 121 TEAFVKHTTNSAHGSTNPFLNWKDIANYNLLLPPIEEQ-----KKMAEILWSMEDNIEKN 175

Query: 189 IRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
            + I+  K+ K+ +++ ++TKG+    K K++ +   G +P++W++
Sbjct: 176 EKLIKKNKQYKKIMINQLLTKGIGHK-KFKETEL---GRIPENWKL 217


>gi|119510903|ref|ZP_01630026.1| type I restriction-modification system, M subunit, putative
           [Nodularia spumigena CCY9414]
 gi|119464431|gb|EAW45345.1| type I restriction-modification system, M subunit, putative
           [Nodularia spumigena CCY9414]
          Length = 471

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 36/43 (83%)

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
           IE L EK+ AL+S+ VTKGL+P V MKDSGIEW+G +P+HWEV
Sbjct: 258 IEKLDEKRTALISHAVTKGLDPSVPMKDSGIEWLGKIPNHWEV 300



 Score = 44.7 bits (104), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 26/37 (70%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD 47
           KDSG++W+G IP HW+V+ +K  TK+  G+ +   ++
Sbjct: 284 KDSGIEWLGKIPNHWEVIKVKHLTKILRGKFTHRPRN 320


>gi|294792925|ref|ZP_06758071.1| putative type I restriction-modification system, S subunit
           [Veillonella sp. 6_1_27]
 gi|294455870|gb|EFG24234.1| putative type I restriction-modification system, S subunit
           [Veillonella sp. 6_1_27]
          Length = 490

 Score = 68.2 bits (165), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/203 (28%), Positives = 97/203 (47%), Gaps = 20/203 (9%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD----IIYIGLEDV 56
           +K +KA P  ++  + +   IP  W    +   +  N  +      D    I  + L+D+
Sbjct: 298 IKKHKALPAIQEDEIPF--DIPSSWCWERLGNISTYNQTKPKIKAIDLDRLIWVLDLDDI 355

Query: 57  ESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP 116
           E  TGK L       +  +    +F KGQILY KL PYL+KA+IA  DG+C+ + +   P
Sbjct: 356 EKNTGKILRYVKAKDKKVSGEKVVFHKGQILYSKLRPYLKKALIALEDGVCTPELV---P 412

Query: 117 KDVLPELLQGWLLSI----DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
            D+     + ++LS+     V   + +   G  M     + + N+ +PIPP+ EQ    E
Sbjct: 413 FDIFGGCNRNYILSVLKSPYVDFGVNSATYGVKMPRVGVETMINLLIPIPPIREQ----E 468

Query: 173 KIIAETVRIDTLITERIRFIELL 195
           +I+ +  +  +LI    RF +L+
Sbjct: 469 RIVKKFDKSHSLIQ---RFKDLV 488


>gi|206603919|gb|EDZ40399.1| Putative Type I Restriction modification system, S subunit
           [Leptospirillum sp. Group II '5-way CG']
          Length = 360

 Score = 68.2 bits (165), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/161 (30%), Positives = 74/161 (45%), Gaps = 7/161 (4%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG 84
           W  VP++                + ++ LE +E  TG  L K+ +   +  S+   F  G
Sbjct: 3   WPAVPLREIAPPKASTQPFPDSFVWHLSLEQIEGDTGAVLAKNYDYSGNVGSSTFYFDTG 62

Query: 85  QILYGKLGPYLRKAIIADFDGICSTQFLVLQ--PKDVLPELLQGWLLSIDVTQRIEAICE 142
            +LY KL PYL K ++ D  GI +T+ + L+  PK + P  L  +L S +  ++      
Sbjct: 63  NVLYSKLRPYLNKVVVPDEPGIATTELIPLRPDPKVLNPRYLAFYLRSPNFVKQASHHVA 122

Query: 143 GATMSHA--DWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           G  M     DW     IP+  PPL+EQ  I E I+ E  RI
Sbjct: 123 GTKMPRVVMDWFWKHKIPL--PPLSEQKRIVE-ILDEADRI 160


>gi|290957397|ref|YP_003488579.1| type I restriction protein fragment [Streptomyces scabiei 87.22]
 gi|260646923|emb|CBG70022.1| putative type I restriction enzyme fragment [Streptomyces scabiei
           87.22]
          Length = 220

 Score = 68.2 bits (165), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 50/162 (30%), Positives = 88/162 (54%), Gaps = 14/162 (8%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDT-STVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           + LE VESG+G+ +   G S+ +D  S  ++F  G +L+GKL  YLRK   AD  G+C+T
Sbjct: 57  VELEQVESGSGRLV---GKSQAADAISLKAVFRPGDVLFGKLRAYLRKFWFADVAGLCTT 113

Query: 110 QFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSH---ADWKGIGNIPMPIPPLAE 166
           +  VL+ +   P +   ++ SI  T+R      GA  +H   +DW  + ++ + IPP  E
Sbjct: 114 EIWVLRAR---PGVDSRFVRSIVETERFIEAASGAYGTHMPRSDWGTVRSLSVDIPPHDE 170

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           Q  I   ++A+  R  +++  R   +   ++ KQ ++  ++T
Sbjct: 171 QRAI-ASVLADIDREISILHAR---LAKARDVKQGMMQQLLT 208


>gi|270594534|ref|ZP_06221501.1| type I restriction-modification system S subunit [Haemophilus
           influenzae HK1212]
 gi|270318347|gb|EFA29502.1| type I restriction-modification system S subunit [Haemophilus
           influenzae HK1212]
          Length = 131

 Score = 68.2 bits (165), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/52 (59%), Positives = 38/52 (73%)

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTE 243
           I LLKE KQ L+   VT+GLNPDV +KDSG+EW+G VP+HWEV     +V E
Sbjct: 6   IALLKEHKQILIQNAVTRGLNPDVPLKDSGVEWIGQVPEHWEVVSMKRVVKE 57



 Score = 53.1 bits (126), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 49/95 (51%), Gaps = 8/95 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRT-----SESGKDIIYIGLEDVESGTGKYLP 65
           KDSGV+WIG +P+HW+VV +KR  K ++G         +  +I ++ + D      KY+ 
Sbjct: 32  KDSGVEWIGQVPEHWEVVSMKRVVKEHSGNGFPIDLQGNNGNIPFLKVSDFSENQDKYIF 91

Query: 66  KDGNSRQSDT---STVSIFAKGQILYGKLGPYLRK 97
           K  NS  +        +I  K  I+  K+G  LRK
Sbjct: 92  KWNNSVTNKVIKQKKWNIVPKNSIVTAKIGEALRK 126


>gi|254416678|ref|ZP_05030429.1| Type I restriction modification DNA specificity domain protein
           [Microcoleus chthonoplastes PCC 7420]
 gi|196176644|gb|EDX71657.1| Type I restriction modification DNA specificity domain protein
           [Microcoleus chthonoplastes PCC 7420]
          Length = 272

 Score = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 85/173 (49%), Gaps = 16/173 (9%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTS----ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSD-- 74
           +P  W+ V   RF  + T +++    ES  +  +I  + +E GTG+ L  D N+ Q D  
Sbjct: 84  LPYGWEWV---RFDSVATIQSNLVKPESYSNYPHIAPDKIEKGTGRLL--DCNTIQEDGV 138

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVT 134
           TS    F  GQILY K+ P L KA++ DF+G+CS     ++   +    L  ++L+    
Sbjct: 139 TSPKHFFFSGQILYSKIRPNLSKAVVIDFEGLCSADMYPIKAY-IYTRYLHFYILTGTFL 197

Query: 135 QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITE 187
           + +        +   + + + N  +P+PPL EQ     +I+A+  R+ +   E
Sbjct: 198 ELVVGYDNRLAIPKVNQQQLNNTVVPVPPLPEQ----HRIVAKVDRLMSFCDE 246


>gi|330971615|gb|EGH71681.1| restriction modification system DNA specificity domain-containing
           protein [Pseudomonas syringae pv. aceris str. M302273PT]
          Length = 233

 Score = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 107/235 (45%), Gaps = 47/235 (20%)

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           M++SG+EW+G VP HW+V               KL  S   S+  G ++   E +N G  
Sbjct: 1   MEESGVEWLGEVPAHWQV--------------CKL--SFRYSVELGKMLD--EKKNTGTS 42

Query: 277 PESYETYQIVDPGEIVFR---FIDLQNDKRSLRSAQ-----VMERGII-TSAYMAVKPHG 327
           P  Y   Q V  G I       ID+++ +    + +     V E G +  +A   +K   
Sbjct: 43  PLPYLRNQDVQWGSININGLPLIDIESSEYERYTVRLGDLLVCEGGDVGRAAIWRIKNSR 102

Query: 328 IDSTYLAWLMR----SYDLCKVFY-------AMGSGLRQSLKFEDVKRLPV--------L 368
           I        +R    S D  + F+       A+G  L +S     +  LP          
Sbjct: 103 IGYQKALHRLRPESPSRDTAEFFFYSLMAAKALGV-LEESDTKATISHLPAEKFRQYRFA 161

Query: 369 VPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            PPI++Q +I +V+  +  R D ++   E  I+LL+ERRS+ I+AAVTG+ID+RG
Sbjct: 162 FPPIEDQQEIASVLGEKLKRSDEIISYAENMIMLLRERRSALISAAVTGKIDVRG 216



 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 96/211 (45%), Gaps = 16/211 (7%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD-----IIYIGLEDVESGTGKY-- 63
           ++SGV+W+G +P HW+V  +     +  G+  +  K+     + Y+  +DV+ G+     
Sbjct: 2   EESGVEWLGEVPAHWQVCKLSFRYSVELGKMLDEKKNTGTSPLPYLRNQDVQWGSINING 61

Query: 64  LPK-DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV--LQPKDVL 120
           LP  D  S + +  TV +   G +L  + G   R AI    +     Q  +  L+P+   
Sbjct: 62  LPLIDIESSEYERYTVRL---GDLLVCEGGDVGRAAIWRIKNSRIGYQKALHRLRPESPS 118

Query: 121 PELLQGWLLSIDVTQRIEAICEG---ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
            +  + +  S+   + +  + E    AT+SH   +         PP+ +Q  I   +  +
Sbjct: 119 RDTAEFFFYSLMAAKALGVLEESDTKATISHLPAEKFRQYRFAFPPIEDQQEIASVLGEK 178

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVT 208
             R D +I+     I LL+E++ AL+S  VT
Sbjct: 179 LKRSDEIISYAENMIMLLRERRSALISAAVT 209


>gi|319428579|gb|ADV56653.1| restriction modification system DNA specificity domain protein
           [Shewanella putrefaciens 200]
          Length = 383

 Score = 67.0 bits (162), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 35/86 (40%), Positives = 55/86 (63%), Gaps = 7/86 (8%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           YIGLE ++SG+ K + + G   + + S   +F KG IL+GK  PYL+KA IA+FDGICS 
Sbjct: 31  YIGLEHLDSGSLK-IKRWGVIAEDNPSFTRVFKKGHILFGKRRPYLKKAAIAEFDGICSG 89

Query: 110 QFLVLQPKD------VLPELLQGWLL 129
             +V++P +      ++P ++Q  L+
Sbjct: 90  DIIVMEPTNSFIAASLIPNIVQSELM 115


>gi|325695186|gb|EGD37087.1| type I restriction-modification system specificty subunit
           [Streptococcus sanguinis SK150]
          Length = 402

 Score = 66.6 bits (161), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 49/162 (30%), Positives = 76/162 (46%), Gaps = 11/162 (6%)

Query: 41  TSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII 100
           TS     +  +  ED+ SG G+ L KD +S+  +   +  F  G  LYGKL PYL   ++
Sbjct: 241 TSSDSSQLPKVEYEDIVSGQGR-LNKDVSSKFDNRKGIH-FKPGYTLYGKLRPYLNNWLL 298

Query: 101 ADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
             F+G+    F V  P    PE +  +L+     Q++     G  M  +DWK +      
Sbjct: 299 PKFEGVALGDFWVFNPNGNNPEFIY-YLIQSSHYQKVANDTSGTKMPRSDWKSVSTTNFA 357

Query: 161 IPP-LAEQVLIREKIIAETVRIDTLIT---ERIRFIELLKEK 198
           +P  + EQV I          +DTLI    ++I  +E+LK+K
Sbjct: 358 LPSTIKEQVAIGSFF----SNLDTLINSYQDKIYQLEILKKK 395


>gi|238921300|ref|YP_002934815.1| hypothetical protein NT01EI_3443 [Edwardsiella ictaluri 93-146]
 gi|238870869|gb|ACR70580.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 323

 Score = 66.6 bits (161), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 46/158 (29%), Positives = 78/158 (49%), Gaps = 9/158 (5%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           +G IP+ W +        L   R +   KDI  + +E +E    +Y   +G +  S TS+
Sbjct: 130 LGEIPEDWSIENFSTLATLRNERINPRTKDIECLCIE-LEHIISEYGQLNGFTETSGTSS 188

Query: 78  V-SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK--DVLPELLQGWLLSIDVT 134
           + ++F+   IL+GKL  YL+K   A   G+CST+  VL+ +    +PE +     ++   
Sbjct: 189 IKNVFSPNDILFGKLRSYLKKYWKATQSGVCSTEIWVLKTELHKAIPEFI---FQTVKTD 245

Query: 135 QRIEAICE--GATMSHADWKGIGNIPMPIPPLAEQVLI 170
           + ++   E  G  M  ADWK I  + +  P + EQ+ I
Sbjct: 246 RFVQTASEAYGTHMPRADWKIIKELQVATPSIEEQIAI 283


>gi|172040757|ref|YP_001800471.1| type I restriction-modification system, specificity subunit
           [Corynebacterium urealyticum DSM 7109]
 gi|171852061|emb|CAQ05037.1| type I restriction-modification system, specificity subunit
           [Corynebacterium urealyticum DSM 7109]
          Length = 397

 Score = 66.6 bits (161), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 95/415 (22%), Positives = 165/415 (39%), Gaps = 42/415 (10%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           I  H+ + P    + L    ++  G+    + L+ +E  TG+ L   G S  +       
Sbjct: 2   IDSHFPLAPFWALSSLVNEVSTPQGE---LVSLDRIEGKTGRLLQGGGESNANGRH---- 54

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELLQGWLLSIDVTQRIEA 139
           F K  +L+GKL PYL K  +AD  G       V +P     P  L   + S   T     
Sbjct: 55  FRKDDVLFGKLRPYLAKYWLADRPGTAQGDIHVYRPTLRTDPRFLAYIVGSDYFTGLANT 114

Query: 140 ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKK 199
              G+ M   +W  +    +P PP   Q  I + +  ET  ID +  +  +   LL E++
Sbjct: 115 SSTGSKMPRVEWPKVAQFRVPFPPRRTQRAIADYLDRETAEIDAMTADLDKMEALLTERR 174

Query: 200 -QALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE------VKPFFALVTELNRKNTKLI 252
            + L S+   +  NP   +      ++G +    +        PFF              
Sbjct: 175 AEILRSWFGEQLNNPRAPLATIAELYIGKMEQPRQKSADEIYAPFFH------------- 221

Query: 253 ESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME 312
            +NI     G I  +   ++M  +P+  + + ++  G++V   ++     R    A+ ++
Sbjct: 222 SANI--RPGGMIDLECSVKHMWFRPDELD-HMLLRKGDVV--VVEGGAAGRPGYIAKSVD 276

Query: 313 RGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLK------FEDVKRLP 366
              I  + +  +P   D     +L   Y L   F      L+ SL        E   R  
Sbjct: 277 GWGIQKSVIRARPFE-DKVIGKYLF--YALTFAFEDGQFDLQASLATLAHFPAEKAARFR 333

Query: 367 VLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           V V  + +Q  +   ++ + + +  ++  I     LL ERR++ IAAAVTGQID+
Sbjct: 334 VPVRSLADQELVVARLDRDLSSLSDMLADITALRDLLAERRAALIAAAVTGQIDI 388


>gi|146281033|ref|YP_001171186.1| hypothetical protein PST_0638 [Pseudomonas stutzeri A1501]
 gi|145569238|gb|ABP78344.1| conserved hypothetical protein [Pseudomonas stutzeri A1501]
          Length = 215

 Score = 66.6 bits (161), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 55/176 (31%), Positives = 91/176 (51%), Gaps = 13/176 (7%)

Query: 259 LSYGNIIQK--LETRNMGL---KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSA--QVM 311
           +SYG++ +   L     GL    PE  + Y I + G++ F       D+    +   Q +
Sbjct: 25  VSYGDVYKNDVLPAEVTGLVQSSPEDQQRYSI-EYGDVFFTRTSETVDEIGFSATCLQEL 83

Query: 312 ERGIITSAYMAVKPHGIDST--YLAWLMRSYDLCKVFY--AMGSGLRQSLKFEDVKRLPV 367
              +     +  +P G   T  +  +  R+  L ++F+   M    R SL  + +K LPV
Sbjct: 84  PNAVFAGFLIRFRPTGKSLTPGFSKYYFRNQGL-RIFFNKEMNLVTRASLSQDLLKLLPV 142

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            +PP+ EQ  I++ ++  TA    L+E+  ++I LLKERRS+ I+AAVTG+ID+RG
Sbjct: 143 TLPPVVEQIKISDFLDRVTAEFASLLEQGIKAIDLLKERRSALISAAVTGKIDVRG 198



 Score = 40.4 bits (93), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 34/52 (65%)

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           +P+ +PP+ EQ+ I + +   T    +L+ + I+ I+LLKE++ AL+S  VT
Sbjct: 140 LPVTLPPVVEQIKISDFLDRVTAEFASLLEQGIKAIDLLKERRSALISAAVT 191


>gi|312879438|ref|ZP_07739238.1| restriction modification system DNA specificity domain [Aminomonas
           paucivorans DSM 12260]
 gi|310782729|gb|EFQ23127.1| restriction modification system DNA specificity domain [Aminomonas
           paucivorans DSM 12260]
          Length = 392

 Score = 66.2 bits (160), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 46/101 (45%), Gaps = 3/101 (2%)

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSI 131
           TS    F  GQ L+GK   Y RK   A+F+GICS   L  +PKD   +LPELL     S 
Sbjct: 60  TSFTRRFVPGQTLFGKRRAYQRKVAYAEFEGICSGDILTFEPKDRKVLLPELLPWICQSN 119

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
                      G+      W  + N   P+PPL EQ  I E
Sbjct: 120 AFFDHALGTSAGSLSPRTSWTALKNFEFPLPPLEEQKRIAE 160


>gi|302343958|ref|YP_003808487.1| restriction modification system DNA specificity domain protein
           [Desulfarculus baarsii DSM 2075]
 gi|301640571|gb|ADK85893.1| restriction modification system DNA specificity domain protein
           [Desulfarculus baarsii DSM 2075]
          Length = 411

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 81/343 (23%), Positives = 135/343 (39%), Gaps = 52/343 (15%)

Query: 69  NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQ 125
           NS    TS    F  GQ L+GK   Y RK   A+F+GICS   L  +PK+   +LPELL 
Sbjct: 54  NSVVDGTSFTRKFVPGQTLFGKRRAYQRKVAYAEFEGICSGDILTFEPKNRKVLLPELLP 113

Query: 126 GWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
               S            G+      W  + +    +PPL EQ  I E + A     D   
Sbjct: 114 FICQSNAFFDHALGTSAGSLSPRTSWTALQDFEFQLPPLDEQKRIAEILWA----ADEAF 169

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF-------- 237
            +  +  + L   K+ L+S +  +G+             +G +P HW +           
Sbjct: 170 NQHQQSNDNLMSVKRTLLSRLTVRGIGQQATQHTR----LGEIPVHWRLATVEDVTSICQ 225

Query: 238 FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
           + L   LN      I   +++   G II   + + + L    + +++ V  G+I+F    
Sbjct: 226 YGLSIPLNESGQYPI-LRMMNYDDGRIIAN-DLKYVDLDDSDFNSFK-VHKGDILF---- 278

Query: 298 LQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY-----DLCKVFYAMGSG 352
                R+  +  V + GI       ++   + ++YL  L         D    +   G G
Sbjct: 279 ----NRTNSADLVGKVGIFD-----LEGDYVFASYLVRLRADEDQILPDFLNYYLNSGLG 329

Query: 353 LRQSLKFE------------DVKRLPVLVPPIKEQFDITNVIN 383
            R+ L +             ++K++ V +PP++EQ  I  V+N
Sbjct: 330 QRRLLAYATPGVSQTNISAGNLKKVLVPLPPMEEQKQIVEVLN 372


>gi|312973901|ref|ZP_07788072.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli 1827-70]
 gi|310331435|gb|EFP98691.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli 1827-70]
          Length = 426

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/267 (22%), Positives = 130/267 (48%), Gaps = 20/267 (7%)

Query: 161 IPPLAEQVLIREKIIAETVRI-DTLITERIRFIELLKEKKQALVSYIVT--KGLNPDVKM 217
           +P L EQ     K IA+ +   D  I+   + +   +++K+AL+  ++T  K L      
Sbjct: 160 LPSLPEQ-----KKIAQILSTWDKAISVTEKLLTNSQQQKKALMQQLLTGKKRLGLPAGS 214

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS-YGNIIQKLETRNMGLK 276
            +  I   G +P  W+      + T+++ KN+  ++  +LS S +   +  L+  N  + 
Sbjct: 215 YEFKITRYGSIPKDWDYPAIKEICTQVSEKNSAAVDHPVLSCSKHDGFVDSLKYFNKKVY 274

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK--PHGIDSTYLA 334
            +    Y+++  G   F F     ++ S+    + + GI++  Y+  +  P  +D++YL 
Sbjct: 275 SDDLSGYRLIHRG--CFGFPSNHIEEGSIGLQNLYDTGIVSPIYVVFRASPTKVDNSYLY 332

Query: 335 WLMRSYDLCKVFYAMGSG---LRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
            ++++    ++F A  +     R SL++++  ++ V +PP+KEQ  I+ V++   A I  
Sbjct: 333 AVLKTDHYKQIFGAATNASVDRRGSLRWKEFNQIHVPLPPLKEQQKISAVLSAADAEITT 392

Query: 392 LVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           L    E+ +  LK+ + + +   +TG+
Sbjct: 393 L----EKKLACLKDEKKALMQQLLTGK 415



 Score = 39.3 bits (90), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 50/201 (24%), Positives = 87/201 (43%), Gaps = 21/201 (10%)

Query: 19  GAIPKHWKVVPIKRF-TKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           G+IPK W    IK   T+++   ++     ++     D    + KY  K   S   D S 
Sbjct: 223 GSIPKDWDYPAIKEICTQVSEKNSAAVDHPVLSCSKHDGFVDSLKYFNKKVYS--DDLSG 280

Query: 78  VSIFAKGQILYGKLGPYLRKAIIAD---FD-GICSTQFLVLQPKDVLPELLQGWLLSIDV 133
             +  +G   +G    ++ +  I     +D GI S  ++V +      ++   +L ++  
Sbjct: 281 YRLIHRG--CFGFPSNHIEEGSIGLQNLYDTGIVSPIYVVFRASPT--KVDNSYLYAVLK 336

Query: 134 TQRIEAICEGATMSHAD------WKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITE 187
           T   + I   AT +  D      WK    I +P+PPL EQ    +KI A     D  IT 
Sbjct: 337 TDHYKQIFGAATNASVDRRGSLRWKEFNQIHVPLPPLKEQ----QKISAVLSAADAEITT 392

Query: 188 RIRFIELLKEKKQALVSYIVT 208
             + +  LK++K+AL+  ++T
Sbjct: 393 LEKKLACLKDEKKALMQQLLT 413


>gi|328951821|ref|YP_004369155.1| Site-specific DNA-methyltransferase (adenine-specific)
           [Desulfobacca acetoxidans DSM 11109]
 gi|328452145|gb|AEB07974.1| Site-specific DNA-methyltransferase (adenine-specific)
           [Desulfobacca acetoxidans DSM 11109]
          Length = 896

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 49/158 (31%), Positives = 76/158 (48%), Gaps = 15/158 (9%)

Query: 23  KHWKVVPIKRFTKLNTGRTSES-GKDIIYIGLEDVESGTGKYLPKDGNSRQ----SDTST 77
           + W+ +P   F +    R   S   D IY+GLE ++       P+D + R+    SD   
Sbjct: 516 EEWQRLPFGAFAESINERVEPSDAGDEIYVGLEHLD-------PQDLHIRRWGKGSDVIG 568

Query: 78  VSI-FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL--QPKDVLPELLQGWLLSIDVT 134
             + F KG +++G+   Y RK  IA FDGICS   +V+  +P+ VLPE L   ++S    
Sbjct: 569 TKLRFRKGDLIFGRRRAYQRKLAIAQFDGICSAHAMVVRAKPEVVLPEFLPFLMVSDRFM 628

Query: 135 QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
            R   I  G+     +WK +     P+P + +Q  I E
Sbjct: 629 NRAVEISVGSLSPTINWKTLKLEKFPLPSIDQQRRIAE 666


>gi|315187183|gb|EFU20940.1| restriction modification system DNA specificity domain [Spirochaeta
           thermophila DSM 6578]
          Length = 554

 Score = 65.5 bits (158), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/109 (35%), Positives = 57/109 (52%), Gaps = 6/109 (5%)

Query: 22  PKHWKVVPIKRFTKLNTGR-TSESGKDIIYIGLEDVESGTGKYL-PKDGNSRQSDTSTVS 79
           PK W+  PI      +T     E GK  +Y+  E +ES TG Y  P   + R+  ++  S
Sbjct: 197 PKGWETEPIGSLVHFDTALIKPEPGKTYLYLAPEHIESNTGNYTGPHPTDGREIGSAKYS 256

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWL 128
            F    +LY KL PYL K ++    GICST+ + L+P    P+LL+ +L
Sbjct: 257 -FTSDHVLYCKLRPYLNKVVLPHTSGICSTELVPLRPG---PKLLREFL 301


>gi|218263899|ref|ZP_03477847.1| hypothetical protein PRABACTJOHN_03537 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222410|gb|EEC95060.1| hypothetical protein PRABACTJOHN_03537 [Parabacteroides johnsonii
           DSM 18315]
          Length = 234

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/140 (32%), Positives = 73/140 (52%), Gaps = 11/140 (7%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           ++S +D+  +GLE +     ++   D N+   D +    F KGQ+L+G+   Y RKA IA
Sbjct: 18  TKSKQDVPIVGLEHLIPDEIRFDAYDINT---DNTFSKRFVKGQVLFGRRRAYQRKAAIA 74

Query: 102 DFDGICSTQFLVLQPKD--VLPELLQGWLLS---IDVTQRIEAICEGATMSHADWKGIGN 156
           +FDGICS    V+Q  +  +LPELL   + +    D   R  A   G+      W+ + +
Sbjct: 75  EFDGICSGDITVIQAIEGKMLPELLPFIIQTPVFFDYANRGSA---GSLSPRVKWEHLAD 131

Query: 157 IPMPIPPLAEQVLIREKIIA 176
               +PPL EQ ++ +K+ A
Sbjct: 132 YEFELPPLEEQKILADKLWA 151


>gi|163801598|ref|ZP_02195496.1| type I restriction-modification system, endonuclease S subunit
           [Vibrio sp. AND4]
 gi|159174515|gb|EDP59317.1| type I restriction-modification system, endonuclease S subunit
           [Vibrio sp. AND4]
          Length = 382

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/197 (30%), Positives = 88/197 (44%), Gaps = 21/197 (10%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDI-IYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFA- 82
           W++V      K  + R   +  D+ IY+GLE ++  +   L    +   SD     +   
Sbjct: 10  WQMVKFGDIAKQISKRVEPNETDLKIYVGLEHLDPDS---LIIKRHGVPSDVKGQKLLVN 66

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ--PKDVLPELLQGWLLSIDVTQRIEAI 140
           KGQI++GK   Y RK  +AD D ICS   +VL+  P  V+PE L  ++ S     R  AI
Sbjct: 67  KGQIIFGKRRAYQRKIAVADCDCICSAHAMVLEANPDKVIPEFLPFFMQSDVFMNRAVAI 126

Query: 141 CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV---RIDTLITERIRFIELLKE 197
            EG+      WK + +    IP + +Q     KII       RI   IT+       L E
Sbjct: 127 SEGSLSPTIKWKVLASQNFKIPSVVQQ----RKIIEAGFLLQRIQEQITD-------LNE 175

Query: 198 KKQALVSYIVTKGLNPD 214
               L + I+ K LN D
Sbjct: 176 SAINLSNSIIQKSLNRD 192


>gi|331018717|gb|EGH98773.1| type I restriction-modification system specificity determinant
           [Pseudomonas syringae pv. lachrymans str. M302278PT]
          Length = 347

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 66/153 (43%), Gaps = 11/153 (7%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESG--KDIIYIGLEDVES---GTGKYLPKDGNSRQ 72
           +G +P  W    +         +   S    + +Y+GLE +     G   +   DG    
Sbjct: 143 LGLVPSGWGCGVLGDVADTTRKQIQPSAMKAETLYVGLEHIPRQSLGLDSWASTDGLE-- 200

Query: 73  SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV-LPELLQGWLLSI 131
              S  S F KG IL+GKL PY  K +IA F G+CST  LV   K       +   L S 
Sbjct: 201 ---SAKSCFEKGDILFGKLRPYFHKIVIAPFAGVCSTDILVCNAKVADYYGFVAMQLFST 257

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
           ++    + +  GA M   +WK + +  + IPP+
Sbjct: 258 ELVAYADRLSNGAKMPRVNWKDLSDYALVIPPV 290


>gi|87124163|ref|ZP_01080013.1| type I site-specific deoxyribonuclease (specificity subunit)
           [Synechococcus sp. RS9917]
 gi|86168732|gb|EAQ69989.1| type I site-specific deoxyribonuclease (specificity subunit)
           [Synechococcus sp. RS9917]
          Length = 128

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 41/116 (35%), Positives = 63/116 (54%), Gaps = 8/116 (6%)

Query: 314 GIITSAYMAVKP--HGIDSTYLAWLMRSYDLCKV----FYAMGSGLRQSLKFEDVKRLPV 367
           G  T+  +  +P    I S +L +L RS    ++     Y  G   R    F  V+    
Sbjct: 6   GFGTTELIVTRPVKEKITSEFLDYLFRSQTFRRLGESEMYGAGGQKRVPDSF--VRDFTS 63

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
            +P I+EQ  +T  ++ ET +ID L+ + ++ I LL+ERRS+ I+A VTGQID+RG
Sbjct: 64  ALPSIEEQSQVTRFLDRETGKIDALIAEQQRLIELLQERRSALISAVVTGQIDVRG 119



 Score = 42.4 bits (98), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 33/53 (62%)

Query: 156 NIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           +    +P + EQ  +   +  ET +ID LI E+ R IELL+E++ AL+S +VT
Sbjct: 60  DFTSALPSIEEQSQVTRFLDRETGKIDALIAEQQRLIELLQERRSALISAVVT 112


>gi|317494153|ref|ZP_07952569.1| type I restriction modification DNA specificity domain-containing
           protein [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316917926|gb|EFV39269.1| type I restriction modification DNA specificity domain-containing
           protein [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 396

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/287 (24%), Positives = 130/287 (45%), Gaps = 22/287 (7%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           S   KD+  + ++ +    G+ L      +Q   S  + F+ G +L+GKL PYL+K I+A
Sbjct: 34  STESKDLPCLEMDSISQEDGRILHIYSAKQQ--VSIKNKFSAGDVLFGKLRPYLKKYILA 91

Query: 102 DFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAI--CEGATMSHADWKGIGNIPM 159
            FDG CS++  VL    +    L      I   + IEA     G+ M  ADW  I +  M
Sbjct: 92  PFDGACSSEIWVLNGLTINNSFL---FCYIQTKKFIEAANKSSGSKMPRADWSVISSEMM 148

Query: 160 PIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKD 219
             P   EQ  I E + +    +D  I    +  +LL + K+ ++  I ++ L      ++
Sbjct: 149 FFPLKEEQNKIAEFLSS----VDEKIMLLNKQYDLLCQYKKGMMQKIFSQELRFKDDNEN 204

Query: 220 SGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGN-IIQKLETRNMGLKPE 278
           S  +W  L     ++K     VT  N++N     + IL++S  + ++ ++   N  +  +
Sbjct: 205 SFPQWSIL-----QLKDIAIRVTRKNKENN----NTILTISGKDGLVDQMTYFNKQIASK 255

Query: 279 SYETYQIVDPGEIVFRFIDLQN-DKRSLRSAQVMERGIITSAYMAVK 324
           +   Y ++  GE  +     Q     +++     E+G++++ Y+  K
Sbjct: 256 NVTGYFLIKKGEFAYNKSYSQGYPMGAIKMLSNYEKGVVSTLYICFK 302


>gi|317130965|ref|YP_004097247.1| restriction modification system DNA specificity domain [Bacillus
           cellulosilyticus DSM 2522]
 gi|315475913|gb|ADU32516.1| restriction modification system DNA specificity domain [Bacillus
           cellulosilyticus DSM 2522]
          Length = 414

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 65/219 (29%), Positives = 102/219 (46%), Gaps = 23/219 (10%)

Query: 25  WKVVPIKRFTKLNTGRTS-ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAK 83
           W++VP K   +  + R   +  K   YIGLE ++S T K + + G     D     + AK
Sbjct: 15  WRLVPFKLMAEHISKRVEPKETKLKYYIGLEHLDSKTLK-IKRHGTP--EDVQGTKLVAK 71

Query: 84  -GQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLLSIDVTQRIEAI 140
            G I++GK   Y  K  I ++D I S   +VL+ ++  ++ ELL  ++ S +   R   I
Sbjct: 72  PGDIIFGKRRAYQGKVAICEWDAIVSAHSMVLRAQEEVIIKELLPFFMQSQEFYNRSLKI 131

Query: 141 CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK-- 198
            EG+      WK +      IPP   Q  I EK+ A          + I   E+L EK  
Sbjct: 132 SEGSLSPTIKWKVLAEEKFIIPPKNIQRDIIEKLNA--------TEDNINCKEILLEKTL 183

Query: 199 --KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
             K+ LV+ ++T+G+N       S    +G +P  WE+K
Sbjct: 184 KYKEKLVNKLLTRGVNHSNYKPSS----IGEIPKDWELK 218


>gi|56419916|ref|YP_147234.1| type I restriction-modification system specificity protein
           [Geobacillus kaustophilus HTA426]
 gi|56379758|dbj|BAD75666.1| type I restriction-modification system specificity protein
           [Geobacillus kaustophilus HTA426]
          Length = 391

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/160 (26%), Positives = 77/160 (48%), Gaps = 3/160 (1%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT-S 76
           +G IPK W +  ++   +    R  ++G+ +  +    ++    K L  +G    S+  S
Sbjct: 188 LGMIPKGWSICELEEIVEKINERV-KAGEHLFSLPYVPIDVLNQKSLMINGYKHGSEAKS 246

Query: 77  TVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDV-LPELLQGWLLSIDVTQ 135
           ++  F KG IL+G + PY  K  IA FDGI  T   VL+PK+      +   +   +   
Sbjct: 247 SLVKFYKGDILFGAMRPYFHKVCIAPFDGITRTTCFVLRPKNNDYYAFVVATIFREETID 306

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
              +  +G+T+ +ADW+ +  + + +PPL       EK++
Sbjct: 307 YANSHSKGSTIPYADWETLSKMKVILPPLQYLKEYNEKVV 346


>gi|302037816|ref|YP_003798138.1| putative type I restriction-modification system, specificity
           protein [Candidatus Nitrospira defluvii]
 gi|300605880|emb|CBK42213.1| putative Type I restriction-modification system, specificity
           protein [Candidatus Nitrospira defluvii]
          Length = 444

 Score = 64.7 bits (156), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 75/344 (21%), Positives = 132/344 (38%), Gaps = 48/344 (13%)

Query: 104 DGICSTQFLVLQPKDVLPELLQGWLLSIDVTQ-RIEAICEGATMSHADWKGIGNIPMPIP 162
           +G  +    +++P   L      + L+    Q +I A   GA+      + +G I +P+P
Sbjct: 106 EGNVNQHVCIIRPSSRLDHRFLTYCLAAPWGQDQIFAGFTGASRQGLGQRDLGEIQIPLP 165

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
               Q  +   + A    ID  +  + R IE L+  +++ ++  + +GLNP V++K SG 
Sbjct: 166 DRTTQEKVIAYLDASCAAIDAAVAAKRRQIEALERTRKSTITRAMVRGLNPAVQLKTSGQ 225

Query: 223 EWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYG-NIIQKLETRNM-------- 273
            W+G +P HW       L+ E               L+YG N   +LE R +        
Sbjct: 226 HWLGNIPTHWTAPSLKRLLIE--------------PLTYGLNEAAELEDRELPRYLRITD 271

Query: 274 -----GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA------ 322
                 L+ +++ +     P E+      + ND    RS   + +  +   Y        
Sbjct: 272 FDESGALRDDTFRSL----PREVAREAPLVTNDVLFARSGATVGKTFLFRDYQGDACFAG 327

Query: 323 ------VKPHGIDSTYLAWLMRS--YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKE 374
                   P  I+  +L    ++  Y+  K      + + Q++       L + +PP+ E
Sbjct: 328 YLIRARTAPWKINPLFLYLFTKTTAYETWKNLTFTQATI-QNISAAKYNYLVIPLPPLSE 386

Query: 375 QFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           Q  I   +    A    L   I + I  L   R S I   VTGQ
Sbjct: 387 QHSICGFVEQCNADFARLTASINRQITTLTAYRKSLIHECVTGQ 430


>gi|153805906|ref|ZP_01958574.1| hypothetical protein BACCAC_00146 [Bacteroides caccae ATCC 43185]
 gi|149130583|gb|EDM21789.1| hypothetical protein BACCAC_00146 [Bacteroides caccae ATCC 43185]
          Length = 370

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 79/344 (22%), Positives = 146/344 (42%), Gaps = 42/344 (12%)

Query: 48  IIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI--FAKGQILYGKLGPYLRKAIIADFDG 105
           I Y+G E ++S    Y+ K G  + S    +    F  GQIL+    P+L+K  IADFDG
Sbjct: 25  IYYVGGEHIDS-CELYVTKKGVIKGSTIGPMFYCGFTAGQILFVTRNPHLKKCSIADFDG 83

Query: 106 ICSTQFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
           ICS +  V++ KD   +  E L   + S D     E    G      +W  + +    +P
Sbjct: 84  ICSEKTFVIETKDESILTQEYLAIIMQSDDFWNYCEENKSGGVNYFLNWSTLADYEFELP 143

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGI 222
           P+ +Q+ I +K+++   R+      +  + +LL   ++ + S  +    NP    K    
Sbjct: 144 PIKQQLEIAQKVMS-AYRL------KQSYKKLLDATREMVKSQFIEMFGNPVTNTKGWKT 196

Query: 223 EWVGLVPDHWEVKPFFALVTELNRK----NTKLIESNILSLSYGNIIQKL-ETRNMGLKP 277
             +       +V P      +L+ K    N  +IESN      G II+K+ E     L  
Sbjct: 197 AKIK------DVAPEMPSKEQLSGKIWLLNLDMIESNT-----GRIIEKVYEDVENALSV 245

Query: 278 ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH--GIDSTYLAW 335
           +S+      D G ++F  +    +K  +      E G+ T+  + ++P    +   +L+ 
Sbjct: 246 QSF------DEGNVLFSKLRPYLNKVVIPD----EPGMATTELVPLRPEPSKLHKVFLSH 295

Query: 336 LMRSYDLCKVFYAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDI 378
           L+R          +  G +   +   +++    ++PP+ +Q + 
Sbjct: 296 LLRGNQFVNYANDIAGGTKMPRMPLTELRNFDCILPPMDKQLEF 339


>gi|326408002|gb|ADZ65069.1| conserved hypothetical protein [Lactococcus lactis subsp. lactis
           CV56]
          Length = 159

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 58/113 (51%), Gaps = 3/113 (2%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           S +   +  +  ED+ +G G+ L KD  SR+ D    ++F    ILYGKL PYL+  + +
Sbjct: 43  SSNNNQLPKVEFEDIIAGEGR-LNKDI-SRKFDDRKGTLFEPDNILYGKLRPYLKNWLFS 100

Query: 102 DFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGI 154
           DF GI    F V + K+  P+ +   L+  D  QR+     G  M  +DWK +
Sbjct: 101 DFKGIALGDFWVFKSKNSEPKFVYS-LIQADNYQRVANDTSGTKMPRSDWKKV 152


>gi|153807715|ref|ZP_01960383.1| hypothetical protein BACCAC_01997 [Bacteroides caccae ATCC 43185]
 gi|160886163|ref|ZP_02067166.1| hypothetical protein BACOVA_04170 [Bacteroides ovatus ATCC 8483]
 gi|160889101|ref|ZP_02070104.1| hypothetical protein BACUNI_01522 [Bacteroides uniformis ATCC 8492]
 gi|149129324|gb|EDM20538.1| hypothetical protein BACCAC_01997 [Bacteroides caccae ATCC 43185]
 gi|156108048|gb|EDO09793.1| hypothetical protein BACOVA_04170 [Bacteroides ovatus ATCC 8483]
 gi|156861568|gb|EDO54999.1| hypothetical protein BACUNI_01522 [Bacteroides uniformis ATCC 8492]
          Length = 376

 Score = 64.3 bits (155), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 82/173 (47%), Gaps = 20/173 (11%)

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSIDVT 134
           + +F  GQILYG    YL+K  +ADF+G+C+    V + KD       LL   +LS D T
Sbjct: 56  IRVFKPGQILYGSRRTYLKKIAVADFEGVCANTTFVFETKDPHAFEQRLLPFIMLSKDFT 115

Query: 135 QRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE----------TVRIDTL 184
               A  +G+T  +  +  + +    +PPL EQ ++ +K+ A            V  D +
Sbjct: 116 TWSIAKSKGSTNPYVLFSDLADFEFELPPLEEQKVLVDKLWAAYRLKEAYKKLLVATDEM 175

Query: 185 ITERIRFIELL--KEKKQAL--VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  + +FIE+      KQ L  V  I+ KG+ P   ++ S +  +     HW+
Sbjct: 176 V--KSQFIEMYYNTHNKQTLESVCPIMNKGITPKY-VESSSVLVINQACIHWD 225


>gi|24371978|ref|NP_716020.1| type I restriction-modification system, S subunit [Shewanella
           oneidensis MR-1]
 gi|24345830|gb|AAN53465.1|AE015486_6 type I restriction-modification system, S subunit [Shewanella
           oneidensis MR-1]
          Length = 439

 Score = 63.9 bits (154), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 85/361 (23%), Positives = 148/361 (40%), Gaps = 46/361 (12%)

Query: 87  LYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDV-TQRIEAICEGAT 145
           L GK   YL+++   D   +   +   L+ K  L      ++ + D     +E +   + 
Sbjct: 93  LVGKNYAYLKQS---DLPALLVQRVARLRAKSNLHSKYLYYMYATDFWLDYVEVVKTNSG 149

Query: 146 MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSY 205
           + H     I N   P PPL EQ    +KI A    +D +I +    I+ LK+ K  ++  
Sbjct: 150 IPHISNGDIKNFRFPFPPLPEQ----QKIAAILTSVDEVIEKTQAQIDKLKDLKSGMMQE 205

Query: 206 IVTKGLN--------PDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNIL 257
           ++TKG+         P ++ KDS    VG +P  WEVKP  ++V        K+I+    
Sbjct: 206 LLTKGVGIKQGDKYVPHIEFKDSP---VGKIPKSWEVKPLNSVV-------LKIIDCEHK 255

Query: 258 SLSYGN-----IIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME 312
           +  Y +     +++    R+  L  +  +        E   R I    D    R A   E
Sbjct: 256 TAPYVDKSEYLVVRTSNVRHGELVLDDMKYTHADGYAEWTNRAIPSLGDVLFTREAPAGE 315

Query: 313 RGII---TSAYMA-----VKPHG--IDSTYLAWLMRSYDLCKVFYAMGSGLRQS-LKFED 361
             ++   T   M      ++P    I S + +  + S       Y    G   S +  ED
Sbjct: 316 SCLVPENTKVCMGQRMVLLRPDANVIFSNFFSLFLTSEAASCAIYERSIGTTVSRINIED 375

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           +KR+P +VPP+ EQ +I+  I      I    EK++     LK  + + +   +TG++ +
Sbjct: 376 IKRIPCIVPPLSEQQEISKAIQSVQNSILNKQEKLQS----LKNLKKALMQDLLTGKVRV 431

Query: 422 R 422
           +
Sbjct: 432 K 432



 Score = 44.3 bits (103), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 51/219 (23%), Positives = 94/219 (42%), Gaps = 25/219 (11%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRF------TKLNTGRTSESGKDIIYIGLEDVE 57
           Y  + ++KDS V   G IPK W+V P+          +  T    +  + ++ +   +V 
Sbjct: 219 YVPHIEFKDSPV---GKIPKSWEVKPLNSVVLKIIDCEHKTAPYVDKSEYLV-VRTSNVR 274

Query: 58  SG-----TGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
            G       KY   DG +  ++ +  S+   G +L+ +  P     ++ +   +C  Q +
Sbjct: 275 HGELVLDDMKYTHADGYAEWTNRAIPSL---GDVLFTREAPAGESCLVPENTKVCMGQRM 331

Query: 113 VLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVL 169
           VL   D   +       +L S   +  I     G T+S  + + I  IP  +PPL+EQ  
Sbjct: 332 VLLRPDANVIFSNFFSLFLTSEAASCAIYERSIGTTVSRINIEDIKRIPCIVPPLSEQQE 391

Query: 170 IREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           I + I +    +   I  +   ++ LK  K+AL+  ++T
Sbjct: 392 ISKAIQS----VQNSILNKQEKLQSLKNLKKALMQDLLT 426


>gi|254190416|ref|ZP_04896924.1| type I restriction-modification system, endonuclease S subunit
           [Burkholderia pseudomallei Pasteur 52237]
 gi|157938092|gb|EDO93762.1| type I restriction-modification system, endonuclease S subunit
           [Burkholderia pseudomallei Pasteur 52237]
          Length = 387

 Score = 63.9 bits (154), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/146 (30%), Positives = 73/146 (50%), Gaps = 5/146 (3%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG 84
           W+   +     +     SESG +  Y+GLE +++ + K   +   +     +T  +F KG
Sbjct: 14  WRFDQMATNVNVRIDNPSESGVEH-YVGLEHLDADSLKI--RRWGTPDDVEATKLMFKKG 70

Query: 85  QILYGKLGPYLRKAIIADFDGICSTQFLVL--QPKDVLPELLQGWLLSIDVTQRIEAICE 142
            I++G+   Y RK  +A+FDGICS   +VL  +P  VLP+ L  ++ S    +R   I  
Sbjct: 71  DIIFGRRRAYQRKLGVAEFDGICSAHAMVLRAKPDVVLPDFLPFFMQSDLFMKRAVEISV 130

Query: 143 GATMSHADWKGIGNIPMPIPPLAEQV 168
           G+     +WK +      +PP+ EQV
Sbjct: 131 GSLSPTINWKTMAIQEFVLPPIDEQV 156


>gi|288937352|ref|YP_003441411.1| restriction modification system DNA specificity domain protein
           [Klebsiella variicola At-22]
 gi|288892061|gb|ADC60379.1| restriction modification system DNA specificity domain protein
           [Klebsiella variicola At-22]
          Length = 430

 Score = 63.9 bits (154), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 39/103 (37%), Positives = 53/103 (51%), Gaps = 4/103 (3%)

Query: 18  IGAIPKHWKVVPIKRFTKL--NTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75
           +G IPK+W +        L  N  ++ +   DI YIGLE +E     ++   GN     +
Sbjct: 225 LGWIPKNWHIRDFSDIAVLIKNNIKSDDICDDIHYIGLEHLER-KHIFITSYGNGSDV-S 282

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
           S  S F KG +L+GKL PY  K  I  F GICST  LV + K+
Sbjct: 283 SNKSAFNKGDLLFGKLRPYFHKVAITPFSGICSTDILVFRAKE 325


>gi|256841218|ref|ZP_05546725.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|256737061|gb|EEU50388.1| conserved hypothetical protein [Parabacteroides sp. D13]
          Length = 369

 Score = 63.5 bits (153), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 11/140 (7%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           ++S +D+  +GLE +     ++   D N+   D +    F KGQ+L+G+   Y RKA IA
Sbjct: 18  TKSKQDVPIVGLEHLIPDEIRFDAYDINT---DNTFSKRFVKGQVLFGRRRAYQRKAAIA 74

Query: 102 DFDGICSTQFLVLQPKD--VLPELLQGWLLS---IDVTQRIEAICEGATMSHADWKGIGN 156
           +FDGICS    V++  +  ++PELL   + +    D   R  A   G+      W+ + +
Sbjct: 75  EFDGICSGDITVIEAIEGKMVPELLPFIIQTPVFFDYANRGSA---GSLSPRVKWEHLAD 131

Query: 157 IPMPIPPLAEQVLIREKIIA 176
               +PPL EQ ++ +K+ A
Sbjct: 132 YEFELPPLEEQKILADKLWA 151


>gi|168464570|ref|ZP_02698473.1| restriction modification system DNA specificity domain [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|195632638|gb|EDX51092.1| restriction modification system DNA specificity domain [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
          Length = 464

 Score = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 54/103 (52%), Gaps = 4/103 (3%)

Query: 18  IGAIPKHWKVVPIKRFTKL--NTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75
           +G +PK W++       +L     ++ +   ++ Y+GLE +E     ++   GN R   +
Sbjct: 259 LGWVPKGWRIESFSEIAQLVKENVKSEDISSEVHYVGLEHLER-KHIFITNYGNGRDV-S 316

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD 118
           S  S F KG +L+GKL PY  K  I  F GICST  LV + K+
Sbjct: 317 SNKSAFNKGDLLFGKLRPYFHKVAITPFSGICSTDILVFRAKE 359


>gi|135207|sp|P06991|T1SD_ECOLX RecName: Full=Type-1 restriction enzyme EcoDI specificity protein;
           Short=S.EcoDI; AltName: Full=Type I restriction enzyme
           EcoDI specificity protein; Short=S protein
 gi|41744|emb|CAA23553.1| hsdS [Escherichia coli]
          Length = 444

 Score = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 78/183 (42%), Gaps = 6/183 (3%)

Query: 7   YPQYKDSGVQW----IGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTG 61
           +P  K+S  Q+    + +IP +W  +   +   + +   S     + I++    +ES TG
Sbjct: 194 FPAEKNSLKQFRNKELPSIPNNWSWMRFDQVADIASKLKSPLDYPNTIHLAPNHIESWTG 253

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLP 121
           K            TS    F  GQI+Y K+ PYL K  IA FDG+CS     +  K +  
Sbjct: 254 KASGYQTILEDGVTSAKHEFYTGQIIYSKIRPYLCKVTIATFDGMCSADMYPINSK-IDT 312

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
             L  W+L+   T           +   + K +  IP+P PPL EQ  I  ++       
Sbjct: 313 HFLFRWMLTNTFTDWASNAESRTVLPKINQKDLSEIPVPTPPLPEQHEIVRRVEQLFAYA 372

Query: 182 DTL 184
           DT+
Sbjct: 373 DTI 375



 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 86/430 (20%), Positives = 167/430 (38%), Gaps = 60/430 (13%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGR--TSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTS 76
           G +P  WK V +    KL+TG+   + +  D  Y      ES +        NS   DTS
Sbjct: 4   GKLPVDWKTVELGELIKLSTGKLDANAADNDGQYPFFTCAESVS------QINSWAFDTS 57

Query: 77  TVSIFAKGQI----LYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSID 132
            V +   G        GK   Y R  +I     +  T+FL              WLL  +
Sbjct: 58  AVLLAGNGSFSIKKYTGKFNAYQRTYVIEPI--LIKTEFLY-------------WLLRGN 102

Query: 133 VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFI 192
           + ++I     G+T+ +     I +I + +P  +EQ LI EK+     ++++      +  
Sbjct: 103 I-KKITENGRGSTIPYIRKGDITDISVALPSPSEQTLIAEKLDTLLAQVESTKARLEQIP 161

Query: 193 ELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW---------------VGLVPDHWEVKPF 237
           ++LK  +QA++++ +   L  + + +++   +               +  +P++W    F
Sbjct: 162 QILKRFRQAVLTFAMNGELTKEWRSQNNNPAFFPAEKNSLKQFRNKELPSIPNNWSWMRF 221

Query: 238 -------FALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
                    L + L+  NT  +  N +    G           G+    +E Y     G+
Sbjct: 222 DQVADIASKLKSPLDYPNTIHLAPNHIESWTGKASGYQTILEDGVTSAKHEFYT----GQ 277

Query: 291 IVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYL-AWLMRSYDLCKVFYAM 349
           I++  I     +  L    +     + SA M      ID+ +L  W++ +        A 
Sbjct: 278 IIYSKI-----RPYLCKVTIATFDGMCSADMYPINSKIDTHFLFRWMLTNTFTDWASNAE 332

Query: 350 GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSS 409
              +   +  +D+  +PV  PP+ EQ +I   +    A  D + +++  ++  +     S
Sbjct: 333 SRTVLPKINQKDLSEIPVPTPPLPEQHEIVRRVEQLFAYADTIEKQVNNALARVNNLTQS 392

Query: 410 FIAAAVTGQI 419
            +A A  G++
Sbjct: 393 ILAKAFRGEL 402


>gi|313107800|ref|ZP_07793974.1| hypothetical protein PA39016_001140001 [Pseudomonas aeruginosa
           39016]
 gi|310880476|gb|EFQ39070.1| hypothetical protein PA39016_001140001 [Pseudomonas aeruginosa
           39016]
          Length = 378

 Score = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 50/151 (33%), Positives = 74/151 (49%), Gaps = 14/151 (9%)

Query: 25  WKVVPIKRFTKLNTG------RTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTV 78
           WKV    RF +L T         SESG +  Y+GLE +++ + K   +   +     +T 
Sbjct: 5   WKVW---RFDQLATNVNVRIDNPSESGMEH-YVGLEHLDADSLKI--RRWGTPDDVEATK 58

Query: 79  SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVL--QPKDVLPELLQGWLLSIDVTQR 136
            +F KG I++G+   Y RK  +A+FDGICS   +VL  +P  VLP  L  ++ S     R
Sbjct: 59  LMFKKGDIIFGRRRAYQRKLGVAEFDGICSAHAMVLRAKPDVVLPAFLPFFMQSDLFMSR 118

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
              I  G+     +WK +      +PPL EQ
Sbjct: 119 AVEISVGSLSPTINWKTMAVQEFVLPPLEEQ 149


>gi|293400128|ref|ZP_06644274.1| restriction modification system DNA specificity domain protein
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291306528|gb|EFE47771.1| restriction modification system DNA specificity domain protein
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 358

 Score = 63.2 bits (152), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 79/350 (22%), Positives = 150/350 (42%), Gaps = 45/350 (12%)

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-DVLPELL 124
           KD +S   D S   +  KG ++Y  +  +     ++ +DGI S  + VL  K  +  E  
Sbjct: 21  KDNSSE--DKSNYKVVRKGDMVYNSMRMWQGANGVSSYDGIVSPAYTVLTAKVSICNEYF 78

Query: 125 QGWLLSIDVTQRIEAICEGATMSHADWK--GIGNIPMPIPPLAEQVLIREKIIAETVRID 182
                +  +        +G T    + K   I  I + +P +AEQ    EK+ +  V +D
Sbjct: 79  AALFKNYKLINEFRKNSQGMTSDTWNLKYPQIETIKVYLPEVAEQ----EKVASMLVTLD 134

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
             I  +   +E LK+ K+ ++  I       ++ M         L P  +E     A+  
Sbjct: 135 KRIAAQATLVEQLKKYKRGVMQRIFR-----NMSM---------LSPSGFETVQLSAIFK 180

Query: 243 ELNRKNTKLIESNIL--SLSYGNIIQK-LETRNMGLKPESYETYQIVDPGEIVFRFIDLQ 299
           +++R+N+     N++  S  YG I Q+    +++ +   +   Y +++ G+ V+      
Sbjct: 181 KISRRNSNEEIKNVITNSAEYGLIPQRDFFDKDIAVDGNT-SNYYVIEHGDFVY------ 233

Query: 300 NDKRS-------LRSAQVMERGIITSAYMA-VKPHGIDSTYLAWLMRSYDLCKVFYAMGS 351
           N ++S           +  ERGII+  Y   V    I+ +YLAW  +S    +  Y  GS
Sbjct: 234 NPRKSNTAPYGPFNRYEREERGIISPLYTCLVLQADIEPSYLAWYFKSDAWYRYIYDNGS 293

Query: 352 -GLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            G+R    S+    ++ +PV++P  + Q  I  +++   +R    + + E
Sbjct: 294 QGVRHDRVSMTDGLLRGIPVIIPSKEAQLKIAKLLDCLESRFQTELSQYE 343



 Score = 40.4 bits (93), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 31/141 (21%), Positives = 61/141 (43%), Gaps = 8/141 (5%)

Query: 262 GNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYM 321
           G ++Q+ E        E    Y++V  G++V+  + +      + S      GI++ AY 
Sbjct: 10  GGVMQRSEIEGKDNSSEDKSNYKVVRKGDMVYNSMRMWQGANGVSSYD----GIVSPAYT 65

Query: 322 AVKPH-GIDSTYLAWLMRSYDLCKVFYAMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFD 377
            +     I + Y A L ++Y L   F     G+     +LK+  ++ + V +P + EQ  
Sbjct: 66  VLTAKVSICNEYFAALFKNYKLINEFRKNSQGMTSDTWNLKYPQIETIKVYLPEVAEQEK 125

Query: 378 ITNVINVETARIDVLVEKIEQ 398
           + +++     RI      +EQ
Sbjct: 126 VASMLVTLDKRIAAQATLVEQ 146


>gi|75907381|ref|YP_321677.1| restriction modification system DNA specificity subunit [Anabaena
           variabilis ATCC 29413]
 gi|75701106|gb|ABA20782.1| Restriction modification system DNA specificity domain protein
           [Anabaena variabilis ATCC 29413]
          Length = 454

 Score = 63.2 bits (152), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 46/166 (27%), Positives = 75/166 (45%), Gaps = 15/166 (9%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGK---DIIYIGLEDVESGTGKYLPKDGNSRQSD 74
           IG IPK W+V+       + +G+ +   K   +++++G E++ES +G+ L    N   + 
Sbjct: 246 IGFIPKSWEVIRFADAISVTSGQVNPKEKPYSEMLHVGSENIESNSGRLLCLQTNQELNI 305

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD--VLPELLQGWLLSID 132
           +S    F    ILY K+ PYL K  + DF+G CS     ++ K+       L  +LLS  
Sbjct: 306 SSGNYYFNNDDILYSKIRPYLNKVALPDFEGTCSADMYPIRSKNGCFNRNFLFHFLLS-- 363

Query: 133 VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
                  I     +S  D  GI  I      L   +LIR  ++ + 
Sbjct: 364 ------DIFRNQAISFQDRTGIPKINR--AQLGSTLLIRPSLLEQN 401


>gi|77166355|ref|YP_344880.1| restriction modification system DNA specificity subunit
           [Nitrosococcus oceani ATCC 19707]
 gi|76884669|gb|ABA59350.1| Restriction modification system DNA specificity domain
           [Nitrosococcus oceani ATCC 19707]
          Length = 425

 Score = 62.8 bits (151), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 80/343 (23%), Positives = 143/343 (41%), Gaps = 37/343 (10%)

Query: 102 DFDGI-CSTQFLVLQPK--DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIP 158
           D  G+ C     +L+P   +   E L        V      +  G T        I   P
Sbjct: 97  DLSGVVCGYHLTLLKPDQDESDGEFLSHLFQLPSVQHYFYILANGITRFGLTADAINEAP 156

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           +  PPL EQ    +KI A    +D +I +    I  LK+ K A++  ++TKG+    + K
Sbjct: 157 LLTPPLPEQ----QKIAAILSSVDDVIEKTRAQIHKLKDLKTAMMQELLTKGIG-HTEFK 211

Query: 219 DSGIEWVGLVPDHWEVK-----PFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNM 273
           DS    VG +P  W +          +V  + +     +ES + +L   N+      R  
Sbjct: 212 DSP---VGRIPVGWSICSAGEVAVAIMVGVVVKPAQYYVESGVPALRSANV------REN 262

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY--------MAVKP 325
           GL  ++ + Y   D  EI+ +   ++ D  ++R+       ++T  +        +  +P
Sbjct: 263 GLTMDNLK-YFSEDSNEILKKSRLIKGDLLTVRTGYPGTTAVVTDEFEGCNCIDVVITRP 321

Query: 326 HG-IDSTYLA-WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
              IDS +   W+   +   +V  A G   +Q     D+K L V+VP + EQ  I N +N
Sbjct: 322 SSRIDSDFFCLWVNSDHGKGQVLKAQGGLAQQHFNVSDMKNLTVVVPSLTEQKAIFNAVN 381

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
             T +I +     E+ + LL + + + +   +TG++ +  E +
Sbjct: 382 SVTKKIAL----TEKRLTLLLDTKKALMQDLLTGKVRVNVEQE 420



 Score = 37.0 bits (84), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 44/205 (21%), Positives = 85/205 (41%), Gaps = 17/205 (8%)

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIES--------NILSLSYGN-IIQKLETRNMGLKPE 278
           VP+ WEVKP   LV   +    K  E+        N   + Y N I   ++      K  
Sbjct: 5   VPEGWEVKPLGKLVDVRSSNIDKKTETSEIPVRLCNYTDVYYNNRITSAIDFMAASAKQR 64

Query: 279 SYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA-VKPHG--IDSTYLAW 335
             + + +     I+ +  +  +D            G++   ++  +KP     D  +L+ 
Sbjct: 65  EIDRFSLEKGDVIITKDSETPDDIAVPSYVSDDLSGVVCGYHLTLLKPDQDESDGEFLSH 124

Query: 336 LMRSYDLCKVFYAMGSGL-RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
           L +   +   FY + +G+ R  L  + +   P+L PP+ EQ  I  ++    + +D ++E
Sbjct: 125 LFQLPSVQHYFYILANGITRFGLTADAINEAPLLTPPLPEQQKIAAIL----SSVDDVIE 180

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQI 419
           K    I  LK+ +++ +   +T  I
Sbjct: 181 KTRAQIHKLKDLKTAMMQELLTKGI 205


>gi|254436045|ref|ZP_05049552.1| Type I restriction modification DNA specificity domain protein
           [Nitrosococcus oceani AFC27]
 gi|207089156|gb|EDZ66428.1| Type I restriction modification DNA specificity domain protein
           [Nitrosococcus oceani AFC27]
          Length = 369

 Score = 62.8 bits (151), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 80/343 (23%), Positives = 143/343 (41%), Gaps = 37/343 (10%)

Query: 102 DFDGI-CSTQFLVLQPK--DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIP 158
           D  G+ C     +L+P   +   E L        V      +  G T        I   P
Sbjct: 41  DLSGVVCGYHLTLLKPDQDESDGEFLSHLFQLPSVQHYFYILANGITRFGLTADAINEAP 100

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           +  PPL EQ    +KI A    +D +I +    I  LK+ K A++  ++TKG+    + K
Sbjct: 101 LLTPPLPEQ----QKIAAILSSVDDVIEKTRAQIHKLKDLKTAMMQELLTKGIG-HTEFK 155

Query: 219 DSGIEWVGLVPDHWEVK-----PFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNM 273
           DS    VG +P  W +          +V  + +     +ES + +L   N+      R  
Sbjct: 156 DSP---VGRIPVGWSICSAGEVAVAIMVGVVVKPAQYYVESGVPALRSANV------REN 206

Query: 274 GLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY--------MAVKP 325
           GL  ++ + Y   D  EI+ +   ++ D  ++R+       ++T  +        +  +P
Sbjct: 207 GLTMDNLK-YFSEDSNEILKKSRLIKGDLLTVRTGYPGTTAVVTDEFEGCNCIDVVITRP 265

Query: 326 HG-IDSTYLA-WLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
              IDS +   W+   +   +V  A G   +Q     D+K L V+VP + EQ  I N +N
Sbjct: 266 SSRIDSDFFCLWVNSDHGKGQVLKAQGGLAQQHFNVSDMKNLTVVVPSLTEQKAIFNAVN 325

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
             T +I +     E+ + LL + + + +   +TG++ +  E +
Sbjct: 326 SVTKKIAL----TEKRLTLLLDTKKALMQDLLTGKVRVNVEQE 364


>gi|329937001|ref|ZP_08286630.1| restriction modification system DNA specificity subunit
           [Streptomyces griseoaurantiacus M045]
 gi|329303608|gb|EGG47493.1| restriction modification system DNA specificity subunit
           [Streptomyces griseoaurantiacus M045]
          Length = 210

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 57/96 (59%), Gaps = 4/96 (4%)

Query: 332 YLAWLMRSY--DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
           YL W +R+   DL     AMGS   +++   D++ L + +PP++ Q  I + I  + AR+
Sbjct: 107 YLLWCLRAMRPDLLGRL-AMGS-THKTIYVPDLQMLRIPLPPMETQEQIVDAIRRQNARV 164

Query: 390 DVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGES 425
           D L +K+++   LL+ERR + I AAVTGQ D+   S
Sbjct: 165 DALTDKVQRQHELLRERRQALITAAVTGQFDVSTAS 200



 Score = 39.3 bits (90), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 37/69 (53%)

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           +P+PP+  Q  I + I  +  R+D L  +  R  ELL+E++QAL++  VT   +      
Sbjct: 142 IPLPPMETQEQIVDAIRRQNARVDALTDKVQRQHELLRERRQALITAAVTGQFDVSTASG 201

Query: 219 DSGIEWVGL 227
            +  E VG+
Sbjct: 202 RNVTEGVGV 210


>gi|288870250|ref|ZP_06409683.1| putative type II restriction-modification enzyme [Clostridium
           hathewayi DSM 13479]
 gi|288867882|gb|EFD00181.1| putative type II restriction-modification enzyme [Clostridium
           hathewayi DSM 13479]
          Length = 889

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/165 (32%), Positives = 85/165 (51%), Gaps = 20/165 (12%)

Query: 50  YIG----LEDVES-GTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFD 104
           Y+G    L+++E  G+ +++PK G        T   ++KG IL   + PYL+K  +AD D
Sbjct: 737 YVGVDNLLQNMEGKGSSQFVPKSG--------TAIAYSKGNILLSNIRPYLKKIWLADND 788

Query: 105 GICSTQFLVLQPKDV-LPELLQGWLLSIDVTQRIE-AICEGATMSHADWKGIGNIPMPIP 162
           G  S   LVL+  D  +      +LL+ D     E    +G  M  AD   + N  +PIP
Sbjct: 789 GGSSGDVLVLKMDDTKISSKYLYYLLATDEFFEYEMQHIKGVKMPRADKASVLNYNVPIP 848

Query: 163 PLAEQVLIREKIIAETVRIDTLITER-IRFIELLKEKKQALVSYI 206
            L +Q    ++I+AE  +I++ IT R +R  +L K+K + L  Y+
Sbjct: 849 SLFKQ----QEIVAEIEKIESEITTRKMRLEDLKKQKGKVLDKYL 889


>gi|302336437|ref|YP_003801644.1| restriction modification system DNA specificity domain protein
           [Olsenella uli DSM 7084]
 gi|301320277|gb|ADK68764.1| restriction modification system DNA specificity domain protein
           [Olsenella uli DSM 7084]
          Length = 525

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/174 (28%), Positives = 78/174 (44%), Gaps = 14/174 (8%)

Query: 20  AIPKHWKVVPIKRFTKLNTGRTSES------GKDIIYIGLEDVESGTGKYLPKDGNSRQS 73
           AIP+ W      RF  ++   +SES        +   + LED+E G+G+ L +     + 
Sbjct: 354 AIPRTWA---WSRFGAISNYGSSESVNPEKIDDEAWVLDLEDIEKGSGRILRRVCGGERR 410

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ-PKDVLPELLQGWLLSID 132
            +S    F  GQ+LY KL PYL K +IA   G C+++ + ++    V P  ++  L+S  
Sbjct: 411 SSSVKRPFCAGQLLYSKLRPYLNKVLIAPEPGYCTSEIIPIELYGTVAPSYIRLVLMSDY 470

Query: 133 VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
                     G  M     +      +PIPP  EQ    E+I +    I TL+T
Sbjct: 471 FLSYANRCSYGVKMPRLGTRDGQGALLPIPPSHEQ----ERIASAAETIATLLT 520


>gi|78358464|ref|YP_389913.1| restriction endonuclease S subunits-like [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78220869|gb|ABB40218.1| Restriction endonuclease S subunits-like protein [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 390

 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/129 (33%), Positives = 57/129 (44%), Gaps = 4/129 (3%)

Query: 69  NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQ 125
           NS    TS    F  GQ L+GK   Y RK   A+F+GICS   L  +PK+   +LPELL 
Sbjct: 54  NSVVDGTSFTRKFVPGQTLFGKRRAYQRKVAYAEFEGICSGDILTFEPKNRKVLLPELLP 113

Query: 126 GWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
               S            G+      W  + +   P+PP+ EQ  I E + A    ++   
Sbjct: 114 FICQSDAFFDHALDTSAGSLSPRTSWTALKDFEFPLPPIDEQKRIAEILWAADEAVEQW- 172

Query: 186 TERIRFIEL 194
           TE  R  EL
Sbjct: 173 TEAYRQAEL 181


>gi|91772548|ref|YP_565240.1| restriction modification system DNA specificity subunit
           [Methanococcoides burtonii DSM 6242]
 gi|91711563|gb|ABE51490.1| Restriction modification system DNA specificity subunit
           [Methanococcoides burtonii DSM 6242]
          Length = 511

 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/184 (25%), Positives = 81/184 (44%), Gaps = 12/184 (6%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           +P  +    +     L + + + SG+ + YIGLE +    G     D        +  + 
Sbjct: 284 LPNGYGWTRLGELHHLKSDKHTGSGESLFYIGLEHISKNQGTLT--DEVKIDVINTVKNS 341

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPEL----LQGWLLSIDVTQR 136
           F KG +LYGKL PYL K  +A+ DG+CST  LV +    +P L     + + LS      
Sbjct: 342 FKKGDLLYGKLRPYLNKVYLANEDGVCSTDILVFES---IPSLDLNYSKYYFLSYKFVND 398

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI---IAETVRIDTLITERIRFIE 193
           +     G  +     K +   P P+  L EQ  I  +I   ++   +++  I + ++  E
Sbjct: 399 MTHNSSGVNLPRVSTKYLQEYPFPLFSLEEQQAIVTEIETRLSVCDKVEQDIEDNLKIAE 458

Query: 194 LLKE 197
            L++
Sbjct: 459 ALRQ 462



 Score = 45.4 bits (106), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 73/169 (43%), Gaps = 22/169 (13%)

Query: 45  GKDIIYIGLEDVESGTGKYLPKDGNSRQSDT------STVSIFAKGQILYGKLGPYLRKA 98
           G+DI++I   D+   + KY+ K    R+S T      S+  +  KG +L+    P    A
Sbjct: 41  GEDILWITPADLSGYSEKYIYK---GRKSITHLGLKNSSARLIPKGSVLFSSRAPIGYIA 97

Query: 99  IIADFDGICSTQ-FLVLQPKDVLP-ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN 156
           I  +   +C+ Q F  L P + L  + L  +L SI   Q  E    G T      K    
Sbjct: 98  IAGN--ELCTNQGFKTLIPSEALNRDFLYYYLKSI--KQLAEGRASGTTFKELSGKAFAE 153

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSY 205
           +P+ +PPL EQ  I         +I+ L +E    I  LK  +Q L  Y
Sbjct: 154 LPLCVPPLPEQRAI-------VSKIEQLFSELDNGIANLKLAQQQLKVY 195


>gi|311278007|ref|YP_003940238.1| restriction modification system DNA specificity domain-containing
           protein [Enterobacter cloacae SCF1]
 gi|308747202|gb|ADO46954.1| restriction modification system DNA specificity domain protein
           [Enterobacter cloacae SCF1]
          Length = 394

 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 78/160 (48%), Gaps = 7/160 (4%)

Query: 44  SGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF 103
           SG +   I ++ +    G+ L    +++Q   S  ++F KG +L+GKL PYLRK I+A F
Sbjct: 237 SGINYPCIEMDCISQRDGQLLTTLDSTQQQ--SIKNVFKKGDVLFGKLRPYLRKYILATF 294

Query: 104 DGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           DG+CS++  V +   +    L  + +  D    +     G+ M  ADW  I +  +  P 
Sbjct: 295 DGVCSSEIWVFKGILINNSYLYQF-IQTDFFINLANKSTGSKMPRADWDTISSTFVFYPC 353

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALV 203
           L EQ  I   + A    +D  I  +   ++ LK  KQ L+
Sbjct: 354 LEEQSKIANFLSA----LDDKIAVKKAELDKLKTWKQGLL 389


>gi|253569551|ref|ZP_04846961.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Bacteroides
           sp. 1_1_6]
 gi|251841570|gb|EES69651.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Bacteroides
           sp. 1_1_6]
          Length = 326

 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 41/128 (32%), Positives = 64/128 (50%), Gaps = 5/128 (3%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
           +GLE +     K+   D ++  + T T   F KGQIL+G+   YL+KA IADFDGICS  
Sbjct: 1   VGLEHLIPQEIKFSGYDVDTENTFTKT---FKKGQILFGRRRAYLKKAAIADFDGICSGD 57

Query: 111 FLVLQ--PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
             V++  P  V P LL   + +        +   G       W+ + +    +PP+ EQ 
Sbjct: 58  ITVIEAIPGKVDPLLLPFIIQNDKFFDYAVSRSAGGLSPRVKWEHLKDYEFDLPPIEEQR 117

Query: 169 LIREKIIA 176
           ++ +K+ A
Sbjct: 118 ILADKLWA 125


>gi|254456858|ref|ZP_05070286.1| type I restriction-modification system, S subunit
           [Campylobacterales bacterium GD 1]
 gi|207085650|gb|EDZ62934.1| type I restriction-modification system, S subunit
           [Campylobacterales bacterium GD 1]
          Length = 365

 Score = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/157 (28%), Positives = 80/157 (50%), Gaps = 5/157 (3%)

Query: 46  KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDG 105
           ++++++G  ++ES  G  +       ++  S   +F +  ILY K+ PYL K +  +F G
Sbjct: 198 QNLVHVGAGNIESQKGTLIDLKTAKEENLISGKFLFDESMILYSKIRPYLMKVVNCNFKG 257

Query: 106 ICSTQFLVLQPKD--VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           +CS     L P D  +  + L   LLS + T+      + A M   + + + +    +PP
Sbjct: 258 LCSADIYPLWPFDNKMQKDFLYHLLLSKNFTEYAILGSQRAGMPKVNREHLFSYRFYLPP 317

Query: 164 LAEQVLIREK---IIAETVRIDTLITERIRFIELLKE 197
           L+EQ  I +K   + AET R++T+  + I  +E LK+
Sbjct: 318 LSEQEQIVQKLNALSAETKRLETIYQKNIEDLEELKK 354


>gi|296328649|ref|ZP_06871166.1| type I restriction-modification system specificity subunit
           [Fusobacterium nucleatum subsp. nucleatum ATCC 23726]
 gi|296154248|gb|EFG95049.1| type I restriction-modification system specificity subunit
           [Fusobacterium nucleatum subsp. nucleatum ATCC 23726]
          Length = 455

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 89/199 (44%), Gaps = 25/199 (12%)

Query: 218 KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS--YGNIIQKLETRNMGL 275
           K++ I W+G +P HWE K    +      KN+ +    +LSLS  YG  +        G 
Sbjct: 8   KETDIPWLGEIPSHWETKKIGKIFDIRKEKNSPVKTKEVLSLSSMYGVSLYSERKEKGGN 67

Query: 276 KP-ESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVK---PHGIDST 331
           KP E+ E Y +  PG+I+   +++      + +      G I+  Y +++          
Sbjct: 68  KPKENLEAYNLCYPGDILVNSMNIVAGSVGISNY----FGAISPVYYSLQNLSEKKYSKY 123

Query: 332 YLAWLMRSYDLCKVFYAMGSGLRQS-------------LKFEDVKRLPVLVPPIKEQFDI 378
           YL +L R+Y+  +    +G G++ S             + ++ +K      PPI+EQ  I
Sbjct: 124 YLEYLFRNYNFQRSLVGLGKGIQMSETEDGRLFTVRMRISWDTLKSQEFPTPPIEEQIQI 183

Query: 379 TNVINVETARID--VLVEK 395
            N ++ +   ID  +L+EK
Sbjct: 184 ANYLDWKINEIDRLILIEK 202



 Score = 56.2 bits (134), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 96/444 (21%), Positives = 181/444 (40%), Gaps = 47/444 (10%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSE-SGKDIIYIGLEDVESGTGKYLP 65
           Y  YK++ + W+G IP HW+   I +   +   + S    K+++ +      S   +   
Sbjct: 4   YDSYKETDIPWLGEIPSHWETKKIGKIFDIRKEKNSPVKTKEVLSLSSMYGVSLYSERKE 63

Query: 66  KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ---PKDVLPE 122
           K GN  + +    ++   G IL   +        I+++ G  S  +  LQ    K     
Sbjct: 64  KGGNKPKENLEAYNLCYPGDILVNSMNIVAGSVGISNYFGAISPVYYSLQNLSEKKYSKY 123

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHAD------------WKGIGNIPMPIPPLAEQVLI 170
            L+    + +  + +  + +G  MS  +            W  + +   P PP+ EQ+ I
Sbjct: 124 YLEYLFRNYNFQRSLVGLGKGIQMSETEDGRLFTVRMRISWDTLKSQEFPTPPIEEQIQI 183

Query: 171 REKIIAETVRIDTLI---TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
              +  +   ID LI    E+I+ +E LK+K      YI    +  ++K K+    ++ L
Sbjct: 184 ANYLDWKINEIDRLILIEKEQIKELENLKQK------YI--DEIYQNIKTKN----FISL 231

Query: 228 VPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQK----LETRNMGLKPESYETY 283
                ++  FF      +R+N  L +S+  ++ YG+I  K     E     +   +Y   
Sbjct: 232 S----KIGTFFK-GGGFSREN--LSDSDYGAILYGDIYTKYNYFFEECISKIDENAYFNS 284

Query: 284 QIVDPGEIVFRFIDLQNDKRSLRSAQVMERGI-ITSAYMAVKPH-GIDSTYLAWLMRSYD 341
           + +D   ++F       +      A V  + I +    +A+KP+      ++A+   + +
Sbjct: 285 KCIDGNVVLFTGSGETKEDIGKNVAYVGTKKIALGGDIIALKPNKNFSPKFIAYFSNTSN 344

Query: 342 LCKVFYAMGS--GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           + K F  M S   +   +    +K + +    I+EQ DI   I+     +  L+  IE  
Sbjct: 345 I-KAFKHMKSTGDIIVHITLGAIKSIKIPFISIEEQKDIVKKIDEYILNLKNLIALIEDK 403

Query: 400 IVLLKERRSSFIAAAVTGQIDLRG 423
           I      + S IA  VTG+ID+R 
Sbjct: 404 IKYFLSLKQSLIAEVVTGKIDVRN 427


>gi|60681330|ref|YP_211474.1| putative type I restriction enzyme, partial [Bacteroides fragilis
           NCTC 9343]
 gi|60492764|emb|CAH07538.1| putative type I restriction enzyme, partial [Bacteroides fragilis
           NCTC 9343]
          Length = 372

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/149 (30%), Positives = 72/149 (48%), Gaps = 22/149 (14%)

Query: 47  DIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGI 106
           + I + LE +  GTG+ L    ++ Q   S  + F+ G +L+GKL PYLRK  +  F+G+
Sbjct: 51  EFICVELESISQGTGELLETFNSAEQK--SIKNKFSPGTVLFGKLRPYLRKFYLPYFEGV 108

Query: 107 CSTQFLVLQPKDVLPELLQGWLLS---IDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           CS++  V++   + P  L  ++ +   I +  +      G+ M  ADW  I    +  PP
Sbjct: 109 CSSEIWVMRSNKIEPAFLYSFIQTPYFISLANQ----SSGSKMPRADWGLIETSKIAYPP 164

Query: 164 LAEQVLIREKIIAETVRID---TLITERI 189
            +          AE V+I     LI ERI
Sbjct: 165 NS----------AERVKIGKFLKLIDERI 183


>gi|85716965|ref|ZP_01047929.1| type I restriction-modification system, endonuclease S subunit
           [Nitrobacter sp. Nb-311A]
 gi|85696244|gb|EAQ34138.1| type I restriction-modification system, endonuclease S subunit
           [Nitrobacter sp. Nb-311A]
          Length = 402

 Score = 60.8 bits (146), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/155 (29%), Positives = 76/155 (49%), Gaps = 8/155 (5%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE ++  + + + + G     +++ +  F  G I++GK   Y RK  +ADF+GICS 
Sbjct: 40  YVGLEHLDPDSLR-IRRWGEPTDVESTKLR-FQPGDIIFGKRRVYQRKVAVADFEGICSA 97

Query: 110 QFLVL--QPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
             +VL  +P  VLP+ L  ++ S    +R  +I  G+     +W  +      +PP+ EQ
Sbjct: 98  HAMVLRAKPGAVLPDFLPFFMQSDLFMERALSISVGSLSPTINWTALAAEEFLLPPIREQ 157

Query: 168 VLIREKIIA----ETVRIDTLITERIRFIELLKEK 198
             + E + A      V+ D L      F  L KE+
Sbjct: 158 SRLVEALSAADKLAEVQHDLLTRSESVFKALFKER 192


>gi|77920514|ref|YP_358329.1| restriction endonuclease S subunit [Pelobacter carbinolicus DSM
           2380]
 gi|77546597|gb|ABA90159.1| restriction endonuclease S subunit [Pelobacter carbinolicus DSM
           2380]
          Length = 394

 Score = 60.5 bits (145), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 42/137 (30%), Positives = 61/137 (44%), Gaps = 6/137 (4%)

Query: 69  NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQ 125
           NS    TS    F  GQ L+GK   Y RK   A+F+GICS   L  +PK+   +L ELL 
Sbjct: 54  NSVADGTSFTRKFVPGQTLFGKRRAYQRKVAFAEFEGICSGDILTFEPKNAKILLAELLP 113

Query: 126 GWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID--- 182
               S            G+      W+ + +   P+PPL EQ  I E + A    ++   
Sbjct: 114 FICQSDAFFDYALDTSVGSLSPRTSWRALKDFEFPLPPLDEQKRIAEILWAADEAVEKYA 173

Query: 183 TLITERIRFIELLKEKK 199
           +L ++   ++E L E  
Sbjct: 174 SLTSDLNAYVETLIENN 190


>gi|118480579|ref|YP_879301.1| hypothetical protein pL2_p3 [Lactococcus lactis subsp. lactis]
 gi|118136319|gb|ABK62798.1| hypothetical protein [Lactococcus lactis subsp. lactis]
          Length = 159

 Score = 60.5 bits (145), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/113 (32%), Positives = 57/113 (50%), Gaps = 3/113 (2%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           S +   +  +  ED+ +G G+ L KD  SR+ D    ++F    ILYGKL PYL+  + +
Sbjct: 43  SSNNNQLPKVEFEDIIAGEGR-LNKDI-SRKFDDRKGTLFEPDNILYGKLRPYLKNWLFS 100

Query: 102 DFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGI 154
           DF GI    F V + K+  P+ +   L+  D  QR+     G  M  + WK +
Sbjct: 101 DFKGIALGDFWVFKSKNSEPKFVYS-LIQADNYQRVANDTSGTKMPRSVWKKV 152


>gi|239621713|ref|ZP_04664744.1| type I restriction-modification system [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|239515588|gb|EEQ55455.1| type I restriction-modification system [Bifidobacterium longum
           subsp. infantis CCUG 52486]
          Length = 151

 Score = 60.5 bits (145), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 47/144 (32%), Positives = 69/144 (47%), Gaps = 8/144 (5%)

Query: 44  SGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADF 103
           S  D+  +  ED+ S  G  L KD   ++   + +  +A G +LYGKL PYL   +   F
Sbjct: 4   SDPDLPQVEYEDIVSDEGT-LNKDLRDKEGGKTGIKFYA-GDVLYGKLRPYLMNWLYPQF 61

Query: 104 DGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           +G+    F VL+  +     L   L+  D  QR+  +  G+ M  ADW  I      +P 
Sbjct: 62  NGVAVGDFWVLRATECDSSFLYR-LVQTDSFQRLANVSSGSKMPRADWNLISQSFFAVPA 120

Query: 164 -LAEQVLIREKIIAETVRIDTLIT 186
             AEQ +I  K +AE   +D LIT
Sbjct: 121 DYAEQRVI-AKSLAE---LDDLIT 140


>gi|281421790|ref|ZP_06252789.1| type I restriction-modification enzyme S subunit [Prevotella copri
           DSM 18205]
 gi|281404148|gb|EFB34828.1| type I restriction-modification enzyme S subunit [Prevotella copri
           DSM 18205]
          Length = 450

 Score = 60.5 bits (145), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 62/134 (46%), Gaps = 5/134 (3%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           LED+E  T K +     + +    T   F KGQILY KL  YL K ++A  DG C+T+ +
Sbjct: 103 LEDIEKDTAKIIQHLNKNERKINGTRHKFQKGQILYSKLRTYLNKVLVAPNDGFCTTEIM 162

Query: 113 VLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
                 +L      ++L S+           G  M         N  +P+PPLAEQ    
Sbjct: 163 AFGSYGILSNNYICYVLRSLYFLDYTLQCGYGVKMPRLSTTDACNGLIPLPPLAEQ---- 218

Query: 172 EKIIAETVRIDTLI 185
           E+I+ E  R+ ++I
Sbjct: 219 ERIVNEIQRLFSII 232


>gi|78046749|ref|YP_362924.1| type I site-specific deoxyribonuclease (specificity subunit)
           [Xanthomonas campestris pv. vesicatoria str. 85-10]
 gi|78035179|emb|CAJ22824.1| type I site-specific deoxyribonuclease (specificity subunit)
           [Xanthomonas campestris pv. vesicatoria str. 85-10]
          Length = 439

 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 91/380 (23%), Positives = 157/380 (41%), Gaps = 53/380 (13%)

Query: 79  SIFAKGQILYGKLGPYLR--KAIIAD--FDGIC--STQFLVLQPKDVLPELLQGWL-LSI 131
           + FA G +   K+ P     K  IA+   +G+   +T+  VL+P   L      +L ++ 
Sbjct: 69  TYFADGDVCIAKITPCFENGKGAIAEGLVNGVAFGTTELHVLRPSATLDTKFLFYLTIAR 128

Query: 132 DVTQRIEAICEGATMSH-------ADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL 184
           D     EA   GA            DW         +P +  Q  I   +  +T RID L
Sbjct: 129 DFRSHGEAEMRGAGGQKRVPEEFLKDWT------PSLPRMDVQQRIARFLDDKTARIDAL 182

Query: 185 ITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS----GIEWVGLVPDHWEVKPF-FA 239
           I ++   +E L+EK++AL++  VT       + K+     G  W+   P  W+VK   FA
Sbjct: 183 IEKKQELLERLEEKRRALITSAVTGESRLRTQAKNKTQKFGSAWLEAAPSDWKVKRLRFA 242

Query: 240 LVTELN-----RKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFR 294
             +  N       + +     I +  +     +L   N  L+     +++     ++   
Sbjct: 243 FESCKNGVWGAEPDDEDSIVCIRAADFDGQSGRLNNGNRTLRTIDNWSFE-----KVRLN 297

Query: 295 FIDLQNDKRSLRSAQVMERGI--------ITSAYMA-VKPH-GIDSTYLAWLMRSYDLCK 344
           F DL  +K      Q++ R +        + S ++A  +P  G    +L +LM +  L +
Sbjct: 298 FGDLILEKSGGGDKQLVGRAVLFDGHTPSVCSNFLARCRPRIGFHHRFLNYLMLAIYLGR 357

Query: 345 VFYAMGSGLRQSLKFEDVKR-----LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
             Y     ++QS   +++       + V +P    Q DI+N ++   A IDV+   + +S
Sbjct: 358 GTYPH---IKQSTGIQNIDTGSYFDMRVAIPEENIQIDISNFLDESVAAIDVIRSCVIRS 414

Query: 400 IVLLKERRSSFIAAAVTGQI 419
           I  L   RS  I  AVTGQ+
Sbjct: 415 IEKLNNFRSIVITDAVTGQL 434



 Score = 46.2 bits (108), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 39/152 (25%), Positives = 74/152 (48%), Gaps = 5/152 (3%)

Query: 280 YETYQIVDPGEIVFRFID--LQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWL 336
           Y  Y     G++    I    +N K ++    V      T+    ++P   +D+ +L +L
Sbjct: 65  YNGYTYFADGDVCIAKITPCFENGKGAIAEGLVNGVAFGTTELHVLRPSATLDTKFLFYL 124

Query: 337 MRSYDLCKVFYA--MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVE 394
             + D      A   G+G ++ +  E +K     +P +  Q  I   ++ +TARID L+E
Sbjct: 125 TIARDFRSHGEAEMRGAGGQKRVPEEFLKDWTPSLPRMDVQQRIARFLDDKTARIDALIE 184

Query: 395 KIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ 426
           K ++ +  L+E+R + I +AVTG+  LR +++
Sbjct: 185 KKQELLERLEEKRRALITSAVTGESRLRTQAK 216


>gi|197249026|ref|YP_002149447.1| type I restriction-modification system, endonuclease S subunit
           [Salmonella enterica subsp. enterica serovar Agona str.
           SL483]
 gi|197212729|gb|ACH50126.1| type I restriction-modification system, endonuclease S subunit
           [Salmonella enterica subsp. enterica serovar Agona str.
           SL483]
          Length = 382

 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 49/157 (31%), Positives = 74/157 (47%), Gaps = 23/157 (14%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDI-IYIGLEDVESGTGKY----LPKDGNSRQSDT 75
           +P+ W++V      K  + R   S  D+ IY+GLE ++  + K     +P D   ++   
Sbjct: 6   LPEGWQMVKFGDIAKHISKRVEPSETDLKIYVGLEHLDPDSLKIKRHGVPADVEGQKL-- 63

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ--PKDVLPELLQGWLLSIDV 133
               +  KGQI++GK   Y RK  +AD+D ICS   +VL+   K V+P  L  ++ S   
Sbjct: 64  ----LVKKGQIIFGKRRAYQRKVAVADWDCICSAHAMVLEENSKMVIPGFLPFFMQSDIF 119

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
             R  AI EG+      WK           LAEQV +
Sbjct: 120 MNRAVAISEGSLSPTIKWK----------VLAEQVFL 146


>gi|77415002|ref|ZP_00791084.1| Type I restriction modification DNA specificity domain protein
           [Streptococcus agalactiae 515]
 gi|77158946|gb|EAO70175.1| Type I restriction modification DNA specificity domain protein
           [Streptococcus agalactiae 515]
          Length = 497

 Score = 60.1 bits (144), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 103/221 (46%), Gaps = 12/221 (5%)

Query: 5   KAYPQYKDSGVQWIGA---IPKHWKVVPIKRFTKLNTGRTSESGKDIIY---IGLEDVES 58
           K Y +  D  ++ +     IP  W+ V ++  + L+        K   Y   + +ED+E 
Sbjct: 47  KPYEKLSDGTIKEVEVPYDIPASWEWVRLRNISSLSFFPNISGDKIPNYSWVLDMEDIEK 106

Query: 59  GTGKYLPKDGNSRQSDTSTVSI-FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP- 116
            TG+ + K+  + +S   +  + F+K  +LY KL P L+K II+D DG  +T+ + ++  
Sbjct: 107 ETGRLVRKNYKTEKSSYKSNKVYFSKDTVLYAKLRPNLKKVIISDEDGFATTELIPIKIF 166

Query: 117 KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
             +  E ++  ++S      I     G  M   +   + +  +P+PPL+EQ  I E+I  
Sbjct: 167 GGISAEYMRYCMISPSYYFNIIKSVYGVKMPRVNATFLNSTLLPLPPLSEQKRIVEQIER 226

Query: 177 ETVRIDTLITERIRFIELLK----EKKQALVSYIVTKGLNP 213
              ++D       +  EL K    + K++++ Y +   L P
Sbjct: 227 ALEKVDAYSESYNKLQELDKSFPDKLKKSILQYAMQGKLVP 267


>gi|217977716|ref|YP_002361863.1| type I restriction enzyme [Methylocella silvestris BL2]
 gi|217503092|gb|ACK50501.1| type I restriction enzyme [Methylocella silvestris BL2]
          Length = 439

 Score = 60.1 bits (144), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 70/280 (25%), Positives = 122/280 (43%), Gaps = 28/280 (10%)

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           +P LA Q +I + +  ET RID LI ++ RF  L  E+ +A +   +        +   S
Sbjct: 142 LPGLAAQKVIADFLDRETARIDQLIEKKERFSALAAERWRATLDAEILGRTTAGKRSLTS 201

Query: 221 GIEWVGLVPDHWEVKPFFALVTELNRKNTKLI------ESNILSLSYGNIIQKLETRNMG 274
           G  ++  VP  W + P   LV         ++      E+ I+ +  G++      +   
Sbjct: 202 GQPYISDVPADWVLTPLKHLVDPRRPVMYGIVLPGPNVENGIMIVKGGDV------KPNR 255

Query: 275 LKPESY-ETYQIVDPGEIVFRFI--DLQNDKRS------LRSAQVMERGIITSAYMAVKP 325
           L P+   +T + ++ G +  R    DL    R       +  A +    +   A      
Sbjct: 256 LSPDRLCKTSREIEAGYVRSRLRGGDLVMAIRGGIGDVEIVPADIEGANLTQDAARIAPR 315

Query: 326 HGIDSTYLAWLMRSYDLCKVFYAMGSGLR----QSLKFEDVKRLPVLVPPIKEQFDITNV 381
           HG+ +    WL  +     VF  +G+G      + +   DV R+ V VPP  EQ  I + 
Sbjct: 316 HGVLNR---WLRYALQAPSVFAPLGAGANGAAVRGVNIFDVDRVLVPVPPTAEQIVIADR 372

Query: 382 INVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           ++++  +I  + EKI     L++E R++ I AAV GQI++
Sbjct: 373 LDIKEQQILRMREKIFDHAKLIQEFRAALITAAVAGQINV 412



 Score = 41.2 bits (95), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 39/148 (26%), Positives = 66/148 (44%), Gaps = 9/148 (6%)

Query: 276 KPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY--MAVKPHGIDSTYL 333
           + ES E Y+ V  G+ V  ++        +        GI++ AY    +    ID  YL
Sbjct: 48  RAESLEGYRQVQRGDFVMNYMLAWKGAYGISEYD----GIVSPAYAVFQIDKSKIDLKYL 103

Query: 334 AWLMRSYDLCKVFYAMGSGL---RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
               RS  +  +F +   G+   R  L  + +    + +P +  Q  I + ++ ETARID
Sbjct: 104 HHRTRSNPMRALFRSRSKGIIDSRLRLYPDALLATEIDLPGLAAQKVIADFLDRETARID 163

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
            L+EK E+   L  ER  + + A + G+
Sbjct: 164 QLIEKKERFSALAAERWRATLDAEILGR 191


>gi|77415160|ref|ZP_00791180.1| Type I restriction modification DNA specificity domain protein
           [Streptococcus agalactiae 515]
 gi|77158789|gb|EAO70080.1| Type I restriction modification DNA specificity domain protein
           [Streptococcus agalactiae 515]
          Length = 271

 Score = 60.1 bits (144), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 46/160 (28%), Positives = 79/160 (49%), Gaps = 5/160 (3%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGK---DIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           IPK W+ V +   + LN   +    K   D   + +ED+E  TG+ + K+  + +S   +
Sbjct: 110 IPKSWEWVRLGNISSLNFFSSISGDKIPNDSWVLDMEDIEKETGRLVRKNYKTEKSSYKS 169

Query: 78  VSI-FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWLLSIDVTQ 135
             I F+K  ILY KL P L+K II+D +G  +T+ L ++   ++  + ++  ++S     
Sbjct: 170 NKISFSKDTILYAKLRPNLKKVIISDENGFATTELLPIKVFGNISLDYIRYCMISPFYYF 229

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
            I     G  M       + +  +P+PPL EQ  I  KI+
Sbjct: 230 NIIQSVYGVKMPRVSSGFLNSTLLPLPPLTEQQRIVSKIL 269


>gi|237755834|ref|ZP_04584432.1| restriction modification system DNA specificity domain protein
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237691999|gb|EEP61009.1| restriction modification system DNA specificity domain protein
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 424

 Score = 59.7 bits (143), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 102/441 (23%), Positives = 183/441 (41%), Gaps = 61/441 (13%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRT------SESGKDIIYIGLEDVESGTGKYLPKDGNSR 71
           IG IP+ W+VV +    ++  G++      +  GK I ++       G  ++        
Sbjct: 12  IGLIPEDWEVVRLGEVAEITMGQSPPGDTYNTYGKGIPFL------QGKAEFGNISPKHI 65

Query: 72  QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSI 131
           +  T  + I  KG +L     P +    IAD D         L  K+ + E L   LL  
Sbjct: 66  KYTTKPLKIAKKGSVLISVRAP-VGDVNIADMDYCIGRGLASLNLKNGINEFLFYSLLFF 124

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
                IE    G+  +  + + +  + +P+PPL EQ  I +  I  TV+    I +  + 
Sbjct: 125 --KHLIEKESYGSVFNAINKENLARLKIPLPPLEEQKAIAD--ILSTVQ--NAIEKAEKV 178

Query: 192 IELLKEKKQALVSYIVTKGLN-----PDVKMKDSGIEWVGLVPDHWEVKPFFALV----- 241
           I   K+ K++++ ++ T G         VK+K+S I   GL+P+HWEV     +V     
Sbjct: 179 INATKQLKKSMMKHLFTYGAVVVDEIDKVKLKESEI---GLIPEHWEVVRLGEVVDLDRG 235

Query: 242 ------TELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
                  E N+ N  LI S I ++  G I       +   K   Y    I    +I    
Sbjct: 236 ISWRKFEEGNKDNGHLIIS-IPNIKDGYI-------DFNSKYNHYLIKHIPKNKQIQLND 287

Query: 296 I-------DLQNDKRSLRSAQVMERGIITSAYM---AVKPHGIDSTYLAWLMRSYDLC-K 344
           I        ++N  R++    +   GI  ++++    VK + +   +L ++  SY    K
Sbjct: 288 ILFVGSSGSIENVGRNVFIENLPFEGIGFASFVFRARVKVNTVIPKFLYFMANSYWFNYK 347

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
            +    S  + + +  + K + + +PP+ EQ  I N++      ID  ++  E+  V L+
Sbjct: 348 DYVRRSSDGKYNFQLTEFKSIKIPLPPLDEQQKIANILTT----IDQKIQAEEKKKVALR 403

Query: 405 ERRSSFIAAAVTGQIDLRGES 425
               + +   +TG+I +R  S
Sbjct: 404 SLFKTLLHQLMTGKIRVRHPS 424


>gi|281421787|ref|ZP_06252786.1| type I restriction-modification system, S subunit [Prevotella copri
           DSM 18205]
 gi|281404164|gb|EFB34844.1| type I restriction-modification system, S subunit [Prevotella copri
           DSM 18205]
          Length = 296

 Score = 59.7 bits (143), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 62/134 (46%), Gaps = 5/134 (3%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           LED+E  T K +     + +    T   F KGQILY KL  YL K ++A  DG C+T+ +
Sbjct: 31  LEDIEKDTAKIIQHLNKNERKINGTRHKFQKGQILYSKLRTYLNKVLVAPNDGFCTTEIM 90

Query: 113 VLQPKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
                 +L      ++L S+           G  M         N  +P+PPLAEQ    
Sbjct: 91  AFGSYGILSNNYICYVLRSLYFLDYTLQCGYGVKMPRLSTTDACNGLIPLPPLAEQ---- 146

Query: 172 EKIIAETVRIDTLI 185
           E+I+ E  R+ ++I
Sbjct: 147 ERIVNEIQRLFSII 160


>gi|94267246|ref|ZP_01290822.1| Restriction modification system DNA specificity domain [delta
           proteobacterium MLMS-1]
 gi|93452076|gb|EAT02762.1| Restriction modification system DNA specificity domain [delta
           proteobacterium MLMS-1]
          Length = 578

 Score = 59.3 bits (142), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 3/95 (3%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGK---DIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           +PK W+ V +   T       +E G+   D   + LED+E  + K L K     +   S+
Sbjct: 101 LPKGWEWVRLGDVTNYGVTEKAEPGETSPDTWVLELEDIEKESSKLLQKVFQRDRQFKSS 160

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
            + F +G +LYGKL PYL K +IAD  G+C+T+ +
Sbjct: 161 KNKFIRGDVLYGKLRPYLDKVLIADASGVCTTEIM 195


>gi|124515159|gb|EAY56670.1| Restriction endonuclease S subunit [Leptospirillum rubarum]
          Length = 142

 Score = 59.3 bits (142), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/95 (36%), Positives = 51/95 (53%), Gaps = 14/95 (14%)

Query: 341 DLCKVFYAMGSGLRQSLKFEDV------------KRLPVLVPPIKEQFDITNVINVETAR 388
           D   V Y + +G  +  K++               R+P+  P + EQ  I + ++ ET+R
Sbjct: 37  DSSYVIYVLTAGRNELFKYDRTAIPQITVDQVASNRIPI--PALSEQLAIASFLDSETSR 94

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           ID L+ +    I LLKE RSS I AAVTG+ID+RG
Sbjct: 95  IDTLISESRTFIDLLKEYRSSLITAAVTGKIDVRG 129



 Score = 50.4 bits (119), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 39/60 (65%), Gaps = 5/60 (8%)

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT-----KGLNP 213
           +PIP L+EQ+ I   + +ET RIDTLI+E   FI+LLKE + +L++  VT     +G  P
Sbjct: 73  IPIPALSEQLAIASFLDSETSRIDTLISESRTFIDLLKEYRSSLITAAVTGKIDVRGFTP 132


>gi|118474615|ref|YP_892156.1| type I restriction-modification system, S subunit [Campylobacter
           fetus subsp. fetus 82-40]
 gi|118413841|gb|ABK82261.1| type I restriction-modification system, S subunit [Campylobacter
           fetus subsp. fetus 82-40]
          Length = 401

 Score = 59.3 bits (142), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 92/435 (21%), Positives = 177/435 (40%), Gaps = 61/435 (14%)

Query: 10  YKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGN 69
           YK + V   G IPK W+VV +    +  T + + +  +++ I  ++       +  K   
Sbjct: 5   YKQTAV---GRIPKEWEVVRLGDVFQRVTRKNTVNSDNVLTISAQNGLIKQENFFTKSVA 61

Query: 70  SRQSDTSTVSIFAKGQILYGK-------LGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
           S+  D S   +  KG+  Y K       +G   R        G+ S  ++  + K+   +
Sbjct: 62  SK--DLSNYILLEKGEFAYNKSYSSGYPMGATKRLNFYN--YGVLSNLYIYFKIKNGNSD 117

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWK----GIGNIPMPIPPLAEQVLIREKIIAET 178
             + +  +  + + I  I +    +H           NI + +PPL EQ    EKI    
Sbjct: 118 FYEQYFEAGLLNKEIHQIAQEGARNHGLLNISVVDFFNILIVLPPLKEQ----EKIAEIL 173

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK--- 235
              D +I+     I+     K AL+  +    L+  ++ K+          D W+ K   
Sbjct: 174 STCDKVISNLDELIKAKTNLKTALMQNL----LSAKIRFKE--------FTDPWQEKFGD 221

Query: 236 PFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
             F  +TE+N+     I +  +S  +G I + L    + +  +S   Y++V  G  +   
Sbjct: 222 KLFKTITEINQNYDLPILA--ISQEFGAIPRNLIDYKVIVSYKSISNYKVVRKGNFII-- 277

Query: 296 IDLQNDKRSLRSAQ-----VMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFYAM 349
                   SLRS Q         GI + AY+ +KP   I   +  +  +S+D  +   + 
Sbjct: 278 --------SLRSFQGGIEYSKYDGICSPAYIILKPIQQIFDNFFKYYFKSHDYIQKLNSK 329

Query: 350 GSGLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERR 407
             G+R  + + F+    + + +P + EQ  I  V++     I++L +K+      LK ++
Sbjct: 330 LEGIRDGKMVSFKQFSEIKIPLPNLAEQQKIAEVLSACDDEINLLKDKLSN----LKLQK 385

Query: 408 SSFIAAAVTGQIDLR 422
              +   +TG++ +R
Sbjct: 386 QGLMQNLLTGKVRVR 400


>gi|282915752|ref|ZP_06323522.1| type-I specificity determinant subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|283768150|ref|ZP_06341065.1| predicted protein [Staphylococcus aureus subsp. aureus H19]
 gi|282320381|gb|EFB50721.1| type-I specificity determinant subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|283462029|gb|EFC09113.1| predicted protein [Staphylococcus aureus subsp. aureus H19]
          Length = 400

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/126 (33%), Positives = 62/126 (49%), Gaps = 4/126 (3%)

Query: 49  IYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICS 108
           I I L+ +E  TG+ L K  NS++  +S  + F    +LYGKL PYL K       G+CS
Sbjct: 46  IDIELDCIEQNTGR-LIKIYNSKEF-SSQKNKFNPQNVLYGKLRPYLNKYYFTKKSGVCS 103

Query: 109 TQFLVLQP--KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
           ++  VL+   +D L  L   + +       + +   G+ M  ADW  + NI +  P L E
Sbjct: 104 SEIWVLKSTKEDKLLNLFLYYFIQTKRYSDVASKSAGSKMPRADWGLVENIRVYFPELCE 163

Query: 167 QVLIRE 172
           Q  I E
Sbjct: 164 QQKIGE 169


>gi|327401773|ref|YP_004342612.1| restriction modification system DNA specificity domain-containing
           protein [Archaeoglobus veneficus SNP6]
 gi|327317281|gb|AEA47897.1| restriction modification system DNA specificity domain protein
           [Archaeoglobus veneficus SNP6]
          Length = 420

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 32/233 (13%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSES----GKDIIYIGLEDVESGTGKYLPKDGNSRQS 73
           IG IP+ W+VV +   TK+N    + +     ++  YI ++ +++   K + K    + +
Sbjct: 10  IGKIPEDWEVVRLGDVTKVNPESINPAKEAPDEEFYYIEIDSIQNSKIKSV-KKIIGKNA 68

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIA--DFDG-ICSTQFLVLQPKDVL--PELLQGWL 128
            +    +  +  ++   + PYL+  +I    +DG ICST F VL+ K+ L  P+ L   L
Sbjct: 69  PSRARRVVRENDVIMSTVRPYLKAFVIVPKKYDGQICSTGFAVLRCKNELIEPKYLLYNL 128

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV-----RIDT 183
                 ++   +  G      +   +  + +P+PPL EQ  I E  I  TV     ++D 
Sbjct: 129 FMDRTIEQCNRLMVGGQYPALNQSHVEQLKIPLPPLPEQRKIAE--ILSTVDEAIQKVDE 186

Query: 184 LI--TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
            I  TER+         K+ L+  ++TKG+    + KD+ I   G +P  WEV
Sbjct: 187 AIVKTERL---------KKGLMQELLTKGIG-HTEFKDTEI---GRIPKEWEV 226


>gi|254172634|ref|ZP_04879309.1| type I restriction modification system, subunit S [Thermococcus sp.
           AM4]
 gi|214033563|gb|EEB74390.1| type I restriction modification system, subunit S [Thermococcus sp.
           AM4]
          Length = 428

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 87/414 (21%), Positives = 172/414 (41%), Gaps = 51/414 (12%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGK-------DIIYIGLEDVESGTGKYLPKDGNS 70
           IG IP+ WKVV ++    + TG T  + +       ++ +I   D+    G     D   
Sbjct: 12  IGEIPRDWKVVRVREIFDVKTGTTPSTKQTDYWENGEMNWITPTDLSKLNGNIYMGDSER 71

Query: 71  RQSDTS----TVSIFAKGQILYGKLGPYLRKAII---ADFDGICSTQFLVLQPKD---VL 120
           + +  +     +S+  KG ++     P    A++   A F+  C      L PKD   ++
Sbjct: 72  KITKKALEDYNLSLLPKGSLILSTRAPVGYIAVLTEEATFNQGCKG----LVPKDQNKII 127

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
           PE    +       Q +E++  G+T        +    +P+PP  EQ     K IAE +R
Sbjct: 128 PEFYAYYFKF--KRQHLESLSGGSTFKELAKAMLERFLVPLPPRLEQ-----KKIAEILR 180

Query: 181 -IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFA 239
            +D  I +    IE  +  K+ L+  ++TKG+  + + K + I   G +P+ W V     
Sbjct: 181 TVDEAIEKTDLAIEKTERLKKGLMLRLLTKGIKHE-RFKKTEI---GEIPEEWRVVRLEE 236

Query: 240 LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVD--------PGEI 291
           +   + R  +K  + N   + Y       +  N+      Y + + +D         G++
Sbjct: 237 ITRRIKRGPSKKTDDNETGVVYVTSDYIDDHGNLNFDNPKYLSLEKIDRLDKYLLEEGDL 296

Query: 292 VFRFIDLQNDKRSLRSAQVME----RGIITSAYMAVK-PHGIDSTYLAWLMRSYDLCKVF 346
           +   I+  N    +    V E    + I+     A+     ++  Y+ +   SY    + 
Sbjct: 297 I---INCVNSLEKIGKVAVFEGYSKKAIVGFNNFALTLVSTVNPYYVKYFFLSYKGKALI 353

Query: 347 YAMGSGLRQSLKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
            ++     Q + F  +D+ RL + +PP+ EQ  I  +++    ++++L ++ E+
Sbjct: 354 KSISKAAVQQVSFSSKDLLRLKIPLPPLPEQKQIAEILSTVDKKLELLRKRREK 407


>gi|311741899|ref|ZP_07715710.1| conserved hypothetical protein [Aeromicrobium marinum DSM 15272]
 gi|311314905|gb|EFQ84811.1| conserved hypothetical protein [Aeromicrobium marinum DSM 15272]
          Length = 113

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 3/91 (3%)

Query: 119 VLPELLQGWLLSIDVTQ-RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
           +LPE L  WLL     Q   +++  G+T+       IG   +P+PP++EQV I +    +
Sbjct: 16  LLPEYL--WLLFTGAMQPYFDSLTNGSTLRTIGMSIIGGFRIPLPPVSEQVQIVQTARDQ 73

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           T +ID L+ E  RFIEL +E++ AL++  VT
Sbjct: 74  TGKIDELMAETARFIELSRERRSALITAAVT 104



 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 40/62 (64%), Gaps = 2/62 (3%)

Query: 364 RLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           R+P+  PP+ EQ  I      +T +ID L+ +  + I L +ERRS+ I AAVTGQID+RG
Sbjct: 54  RIPL--PPVSEQVQIVQTARDQTGKIDELMAETARFIELSRERRSALITAAVTGQIDVRG 111

Query: 424 ES 425
            +
Sbjct: 112 AA 113


>gi|296106107|ref|YP_003617807.1| hypothetical protein lpa_00830 [Legionella pneumophila 2300/99
           Alcoy]
 gi|295648008|gb|ADG23855.1| hypothetical protein lpa_00830 [Legionella pneumophila 2300/99
           Alcoy]
          Length = 448

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 76/341 (22%), Positives = 145/341 (42%), Gaps = 24/341 (7%)

Query: 100 IADFDGICSTQFLV---LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHAD--WKGI 154
           ++D  G CS  + +   + P    P+    +L ++     IE++ +G      D  WK I
Sbjct: 91  VSDSRGKCSPVYSIAIPINPNAAYPKFWGYYLRNLATAGFIESLAKGIRERSTDFRWKDI 150

Query: 155 GNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKG--LN 212
            N+ +  P    Q  I + +  ET RID LI +++  I +LKEK  ALV+  V +G  + 
Sbjct: 151 SNLLVNFPNYEIQKGIADFLDHETDRIDQLIEKKVGLISVLKEKSTALVTENVLQGHRVY 210

Query: 213 PDVKMKDSGIEWVGLVPDHWE-----VKPFFALVTELNRKNTKLIESNILSLSYGNIIQK 267
           P+    +         PD        +K F      L+ K    +E + + +   +    
Sbjct: 211 PEKTSAEKYTHPDKFWPDGLNGLLQPLKFFCEETASLSDKTDPNMEIHYIDIGNVSFADG 270

Query: 268 LE-TRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERG----IITSAYMA 322
           L+ +     K       Q++   +++   +     +  L++   +++     I ++ +  
Sbjct: 271 LKGSAKYLFKDAPSRARQVLRMHDVIISTV-----RTYLKACAYIDKDLPNLIASTGFCV 325

Query: 323 VKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPPIKEQFDITN 380
           ++P+  I   YL   ++S            G+   ++  + +K L + VP +  Q  I++
Sbjct: 326 LRPNDKIHPKYLYRAIQSDPFISGVVVRSEGVSYPAVNDKMIKALKIPVPDLGLQKSISD 385

Query: 381 VINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            I  E   +      IE+SI LL   +SS I  AVTG++D+
Sbjct: 386 KIEQEIHSVTQTTRLIEKSIDLLSSFKSSLITEAVTGKLDI 426



 Score = 45.1 bits (105), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 73/174 (41%), Gaps = 17/174 (9%)

Query: 47  DIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFD-- 104
           DI  +   D   G+ KYL KD  SR        +     ++   +  YL+     D D  
Sbjct: 261 DIGNVSFADGLKGSAKYLFKDAPSRAR-----QVLRMHDVIISTVRTYLKACAYIDKDLP 315

Query: 105 -GICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
             I ST F VL+P D + P+ L   + S      +    EG +    + K I  + +P+P
Sbjct: 316 NLIASTGFCVLRPNDKIHPKYLYRAIQSDPFISGVVVRSEGVSYPAVNDKMIKALKIPVP 375

Query: 163 PLAEQVLIREKIIAETVRIDTLITERIRFIE----LLKEKKQALVSYIVTKGLN 212
            L  Q  I +KI  E       +T+  R IE    LL   K +L++  VT  L+
Sbjct: 376 DLGLQKSISDKIEQEIHS----VTQTTRLIEKSIDLLSSFKSSLITEAVTGKLD 425



 Score = 44.3 bits (103), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 43/192 (22%), Positives = 84/192 (43%), Gaps = 14/192 (7%)

Query: 232 WEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNM-GLKPESYET-YQIVDPG 289
           W +K F  L  +LNR    + +  +++     ++     R M G      E  YQ V+P 
Sbjct: 18  WHIKRFKYLFKKLNR--PVMDDDGVITAFRDGLVTLRSNRRMDGFTFADKEIGYQGVEPN 75

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAY---MAVKPHGIDSTYLAWLMRSYDLCKVF 346
           ++V   +D       +  +    RG  +  Y   + + P+     +  + +R+       
Sbjct: 76  DLVIHAMDSFAGAIGVSDS----RGKCSPVYSIAIPINPNAAYPKFWGYYLRNLATAGFI 131

Query: 347 YAMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLL 403
            ++  G+R+     +++D+  L V  P  + Q  I + ++ ET RID L+EK    I +L
Sbjct: 132 ESLAKGIRERSTDFRWKDISNLLVNFPNYEIQKGIADFLDHETDRIDQLIEKKVGLISVL 191

Query: 404 KERRSSFIAAAV 415
           KE+ ++ +   V
Sbjct: 192 KEKSTALVTENV 203


>gi|332686985|ref|YP_004456759.1| type I restriction-modification system, specificity subunit S
           [Melissococcus plutonius ATCC 35311]
 gi|332370994|dbj|BAK21950.1| type I restriction-modification system, specificity subunit S
           [Melissococcus plutonius ATCC 35311]
          Length = 328

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 132/294 (44%), Gaps = 30/294 (10%)

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
           D+ +  E    G+T      K I ++ + IP + EQ    +KI     ++D +IT +   
Sbjct: 46  DLKKYGEKNGAGSTFIEVSGKQISHMSIIIPEIEEQ----QKIGNFLKQLDDIITLQQHK 101

Query: 192 IELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTE-----LNR 246
           +ELLK+ KQ  +  +  K      +++ +G  + G     WE + F  +V       L+R
Sbjct: 102 LELLKQMKQGYLQKMFPKNEEDKPEIRFAG--YTGA----WEQRKFGDMVERVKSYSLSR 155

Query: 247 KNTKLIESNILSLSYGNIIQKLETRNMGLKPE---SYETYQIVDPGEIVFRFIDLQNDKR 303
               L +++I  + YG+I  K+  R   L       Y+ Y+ +  G+++    D   D +
Sbjct: 156 DVETLEDTDIKYVHYGDIHTKVADRVTKLSNLPFIKYDDYEFIQKGDVIV--ADASEDYK 213

Query: 304 SLRSAQVM-----ERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQ-SL 357
            + +  V+      + +     +A++P  +DS +L +LM S    K  Y +G+G++   +
Sbjct: 214 GIATPSVIIEDVGYKLVAGLHTIALRPFDMDSVFLYYLMNSNSFRKHGYRVGTGMKVFGI 273

Query: 358 KFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
            + ++       P I EQ  I  ++     +ID  +   +  + LLK+ +  ++
Sbjct: 274 SYSNILNFETYFPQIDEQKKIGWML----LKIDDSIALHQHKLELLKQMKQGYL 323


>gi|282865356|ref|ZP_06274408.1| hypothetical protein SACTEDRAFT_4953 [Streptomyces sp. ACTE]
 gi|282559829|gb|EFB65379.1| hypothetical protein SACTEDRAFT_4953 [Streptomyces sp. ACTE]
          Length = 107

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/72 (40%), Positives = 42/72 (58%)

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLK 196
           +E +  G ++ H     +    MP PPL EQ  +   + AET +IDTLI E  RFIEL +
Sbjct: 27  LEPLFTGVSVPHVSEWQVRKFKMPFPPLDEQRCMARHLDAETAKIDTLIAESERFIELAR 86

Query: 197 EKKQALVSYIVT 208
           E++ AL++  VT
Sbjct: 87  ERRSALITAAVT 98



 Score = 56.2 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 29/64 (45%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           V++  +  PP+ EQ  +   ++ ETA+ID L+ + E+ I L +ERRS+ I AAVTGQID+
Sbjct: 44  VRKFKMPFPPLDEQRCMARHLDAETAKIDTLIAESERFIELARERRSALITAAVTGQIDV 103

Query: 422 RGES 425
            GE+
Sbjct: 104 -GEA 106


>gi|147920567|ref|YP_685636.1| type I restriction modification system, specificity subunit
           [uncultured methanogenic archaeon RC-I]
 gi|110621032|emb|CAJ36310.1| type I restriction modification system, specificity subunit
           [uncultured methanogenic archaeon RC-I]
          Length = 449

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/252 (24%), Positives = 118/252 (46%), Gaps = 27/252 (10%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGT 60
           ++H K    YK++    +G IP+ W +V IK   +  T +     +   Y    DV S +
Sbjct: 14  LEHRKTDDGYKETP---MGRIPEEWSIVSIKNIVE-KTEQIDPQKQPDKYFKYIDVSSVS 69

Query: 61  GKYLP----KDGNSRQSDTSTVSIFAKGQILYGKLGPYLRK-AIIAD-FDG-ICSTQFLV 113
            + L      +     + +    I     I++  + P L++ AII D  +G +CST F V
Sbjct: 70  NESLKVVSVNEFKGINAPSRARRIVRTDDIIFATIRPNLKRVAIICDDLEGQLCSTAFCV 129

Query: 114 LQPKDVLPELLQGWLLSIDVT--QRIEAICE---GATMSHADWKGIGNIPMPIPPLAEQV 168
           L+    +  + + + +   VT  + I  +C+   G+         + +  + +PP++EQ 
Sbjct: 130 LR---CMKNIAEPYFVFQTVTTDRFIGKLCDLQCGSGYPAVTDNDLLDQQILLPPISEQ- 185

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLV 228
               KI A    +D+LI E  R +    + K+ L+   +T+G+  +V+++D+ +   G++
Sbjct: 186 ---RKIAAILGTLDSLIEETDRVVARTGQLKKGLIQEFLTEGMG-NVELEDTAL---GMI 238

Query: 229 PDHWEVKPFFAL 240
           P HW+  PF  L
Sbjct: 239 PKHWKCVPFATL 250


>gi|159901786|ref|YP_001548031.1| restriction modification system DNA specificity subunit
           [Herpetosiphon aurantiacus ATCC 23779]
 gi|159894825|gb|ABX07903.1| restriction modification system DNA specificity domain
           [Herpetosiphon aurantiacus ATCC 23779]
          Length = 418

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/189 (28%), Positives = 90/189 (47%), Gaps = 17/189 (8%)

Query: 11  KDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDII---YIGLEDVESGTGKYLPKD 67
           +D+    I  +P HW V  +K   K  + +   +        Y GL+ +  G  +  PK 
Sbjct: 4   EDTTTSSIWDLPSHWGVKKLKLIAKEISQQIKPADNPSTVYNYWGLDAITKGQFQE-PKQ 62

Query: 68  GNSRQSD-TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQ 125
              + S+  ST   F + QI+Y KL PYL K I+    GI +T+++V++P  +V+     
Sbjct: 63  NLVKGSNIESTCVTFTENQIIYSKLRPYLNKVIVPSIPGIGTTEWIVVEPDANVVDRKYL 122

Query: 126 GWLLS----IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPL---AEQVLIREKIIAET 178
            ++L     +    R E I  GA M         N P+P+P L   A  + I++ I+   
Sbjct: 123 AYVLRSPAFLRYVSRGENI-NGARMPRLRKDSFWNFPIPLPSLSNPARSLQIQQSIV--- 178

Query: 179 VRIDTLITE 187
           VRI++L++E
Sbjct: 179 VRIESLLSE 187


>gi|167718506|ref|ZP_02401742.1| putative type I restriction enzyme specificity protein
           [Burkholderia pseudomallei DM98]
 gi|167814674|ref|ZP_02446354.1| putative type I restriction enzyme specificity protein
           [Burkholderia pseudomallei 91]
          Length = 111

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/100 (35%), Positives = 58/100 (58%), Gaps = 1/100 (1%)

Query: 323 VKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVI 382
           V+ H     YL ++++S     +  ++ S +   +   D+    V +PP +EQ  I   +
Sbjct: 4   VQMHDNVPKYLWYMLQSLKHIFILNSLKSAV-PGVDRNDIHPAIVCLPPAEEQPAIVAFL 62

Query: 383 NVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           + E +++D L    E++I LLKERRS+ IAAAVTG+ID+R
Sbjct: 63  DAEISKLDALRADAERAIDLLKERRSALIAAAVTGKIDVR 102


>gi|300727766|ref|ZP_07061150.1| type I restriction-modification system, endonuclease S subunit
           [Prevotella bryantii B14]
 gi|299774976|gb|EFI71584.1| type I restriction-modification system, endonuclease S subunit
           [Prevotella bryantii B14]
          Length = 375

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/186 (31%), Positives = 92/186 (49%), Gaps = 18/186 (9%)

Query: 32  RFTKLNTGRT-----SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQI 86
           RF K+    T     +ES K+  YIGLE ++S   + + + G S  +      I  KG I
Sbjct: 4   RFDKIAFNSTAKKTPTESDKEH-YIGLEHIDSECLE-ITRWG-SNVAPIGEKLIMKKGDI 60

Query: 87  LYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWLLSIDV-TQRIEAICEGA 144
           L+GK   Y RK  IA FDGI S   +VL+P ++V+ +    + +S D+  +R   I  G 
Sbjct: 61  LFGKRRAYQRKLAIAPFDGIFSAHGMVLRPNEEVVDKNYFPFFMSSDLFMERAVQISVGG 120

Query: 145 TMSHADWKGIGNIPMPIPPLAEQVLIREKIIA-----ETVRIDTLITERI---RFIELLK 196
                +WK +     P+P LAEQ ++ +K+ A     E+ +     TE +   +FIE+  
Sbjct: 121 LSPTINWKDLREQEFPLPSLAEQKVLADKLWAAYRLKESYKKLLAATEEMVKSQFIEMFY 180

Query: 197 EKKQAL 202
            +K  L
Sbjct: 181 NEKYPL 186


>gi|257893690|ref|ZP_05673343.1| type I restriction-modification system specificity subunit
           [Enterococcus faecium 1,231,408]
 gi|257830069|gb|EEV56676.1| type I restriction-modification system specificity subunit
           [Enterococcus faecium 1,231,408]
          Length = 409

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 75/344 (21%), Positives = 145/344 (42%), Gaps = 23/344 (6%)

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQ 135
           S+  I   G +L+         AI+A  +G  +  F  + P +   +    +  + ++ +
Sbjct: 76  SSAKILPIGTVLFTSRAGIGNTAILAK-EGTTNQGFQSIVPHENKLDSYFIFSRTHELKR 134

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
             E    G+T +    K +  +P+ IP + EQ    +KI     ++D  IT   R ++LL
Sbjct: 135 YGEVTGAGSTFAEVSGKQMAKMPILIPYIDEQ----QKIGIFFKKLDDTITLHQRKLDLL 190

Query: 196 KEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLI--E 253
           KE K+  +  +      P    K   I + G   D WE +     +    +KN   I  +
Sbjct: 191 KETKKGFLQKMF-----PKNGAKVPEIRFPGFTED-WEARKLIDYLDVSTQKNKDEIYDK 244

Query: 254 SNILSLSYG-NIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVME 312
            ++LS+S    I+ ++E +       S   Y +V+ G+IV+    L+ +   +      +
Sbjct: 245 GDVLSVSGDCGIVNQIEFQGRSFAGVSVANYGVVETGDIVYTKSPLKANPYGIIKTNKGK 304

Query: 313 RGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYA---MGSGLRQSLKFEDVKRL--PV 367
            GI+++ Y   KP  I       +    D+    Y    +  G +  +K  D   L   V
Sbjct: 305 TGIVSTLYAVYKPKQITDPEFVQIYFEQDVRMNNYMRPLVNKGAKNDMKVSDENALKGEV 364

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
           + P ++EQ  I++       +++ L+   ++ + LLKE +  F+
Sbjct: 365 MFPKLEEQRRISSYF----EQLNNLITLHQRELDLLKETKKGFL 404


>gi|325832692|ref|ZP_08165455.1| type I restriction modification DNA specificity domain protein
           [Eggerthella sp. HGA1]
 gi|325485831|gb|EGC88292.1| type I restriction modification DNA specificity domain protein
           [Eggerthella sp. HGA1]
          Length = 393

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 34/100 (34%), Positives = 51/100 (51%), Gaps = 2/100 (2%)

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDV 133
           D  + +++  G  L   + PYL+KA +AD  G CST  LV  P  V P  L  WL++ D 
Sbjct: 263 DDGSGTLYHPGDTLMSNIRPYLKKAWLADRKGTCSTDVLVFHPTSVEPGYLY-WLIASDA 321

Query: 134 TQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
             R + +  +G+ M   D K I  +P+ +P   EQ  I +
Sbjct: 322 FVRYVMSAAKGSKMPRGDKKHIMEMPLLLPNKDEQRKIDD 361


>gi|224457361|ref|ZP_03665834.1| type I restriction-modification system, subunit S [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|254370730|ref|ZP_04986735.1| predicted protein [Francisella tularensis subsp. tularensis FSC033]
 gi|151568973|gb|EDN34627.1| predicted protein [Francisella tularensis subsp. tularensis FSC033]
 gi|282159469|gb|ADA78860.1| type I restriction-modification system, subunit S [Francisella
           tularensis subsp. tularensis NE061598]
          Length = 225

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 37/123 (30%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+ LE++E  TG+ +       +   S+   F KG +LYGKL PYL K   ++FD + +T
Sbjct: 103 YVVLENIEGNTGRLIDFCETQGKEIKSSKVEFKKGMVLYGKLRPYLNKVWFSEFDDVATT 162

Query: 110 QFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN--IPMPIPPL 164
           + L   P D   +    ++ + LS    QR+   C G+ M       + +    +P+PPL
Sbjct: 163 EILPFYPIDNTRLNMIFVKYYFLSSSYLQRVMRNCSGSRMPRLTTAFLKSEEAYIPLPPL 222

Query: 165 AEQ 167
             Q
Sbjct: 223 PIQ 225


>gi|254875064|ref|ZP_05247774.1| restriction modification system DNA specificity subunit
           [Francisella tularensis subsp. tularensis MA00-2987]
 gi|254841063|gb|EET19499.1| restriction modification system DNA specificity subunit
           [Francisella tularensis subsp. tularensis MA00-2987]
          Length = 222

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 37/123 (30%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+ LE++E  TG+ +       +   S+   F KG +LYGKL PYL K   ++FD + +T
Sbjct: 100 YVVLENIEGNTGRLIDFCETQGKEIKSSKVEFKKGMVLYGKLRPYLNKVWFSEFDDVATT 159

Query: 110 QFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN--IPMPIPPL 164
           + L   P D   +    ++ + LS    QR+   C G+ M       + +    +P+PPL
Sbjct: 160 EILPFYPIDNTRLNMIFVKYYFLSSSYLQRVMRNCSGSRMPRLTTAFLKSEEAYIPLPPL 219

Query: 165 AEQ 167
             Q
Sbjct: 220 PIQ 222


>gi|78046066|ref|YP_362241.1| type I site-specific deoxyribonuclease (specificity subunit)
           [Xanthomonas campestris pv. vesicatoria str. 85-10]
 gi|78034496|emb|CAJ22141.1| type I site-specific deoxyribonuclease (specificity subunit)
           [Xanthomonas campestris pv. vesicatoria str. 85-10]
          Length = 419

 Score = 57.4 bits (137), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 86/202 (42%), Gaps = 18/202 (8%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGR---TSESGKDIIYIGLEDVESGTGKY 63
           +P+++D+           W   P+ +  ++ +G+   T     D  ++G E++ES TG  
Sbjct: 221 FPEFRDA---------PEWAERPLCQVIEVASGQVDPTEAPYCDFPHVGGENIESETGSL 271

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP--KDVLP 121
           +          TS   +F +  +LY K+ P L K  + DF+GICS     ++P   D+  
Sbjct: 272 VGLKSAREDGVTSGKYLFDEKDVLYSKIRPILNKVAVPDFNGICSADIYPIRPSSSDITR 331

Query: 122 ELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRI 181
           + L   L S    +      E   +   + + +      +P   EQ  I + + +    +
Sbjct: 332 QFLVYLLRSASFVEYATKHSERGKIPKINREALAAYGARLPQQVEQQRIADCLFS----V 387

Query: 182 DTLITERIRFIELLKEKKQALV 203
           DT IT     + +LK  KQ L+
Sbjct: 388 DTAITAESAQLTVLKTHKQGLM 409


>gi|206603725|gb|EDZ40205.1| Putative Type I restriction modification system, specificity
           protein [Leptospirillum sp. Group II '5-way CG']
          Length = 533

 Score = 57.0 bits (136), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 75/166 (45%), Gaps = 17/166 (10%)

Query: 18  IGAIPKHWKVVPIKRFTKLN--TGRTSESGKDIIYIGLEDVESGTGKYLPKDGNS----R 71
           +G IP+ W++  +  F   +  + R +E  +   YI LE        ++P+   S    +
Sbjct: 334 LGEIPRGWRIGTLGEFATRSRQSIRPNEIKEGTPYIALE--------HMPRRCISLFEWK 385

Query: 72  QSDT--STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWL 128
            +D   S    F KG IL+GKL  Y  K  +A  +G+CST  LV+ P K  L   + G +
Sbjct: 386 MADEVESNKFEFNKGDILFGKLRSYFHKVGVAPVNGVCSTDILVIAPQKQELFGFVLGHV 445

Query: 129 LSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
            S    Q  +    G  M   +W+ +    + +PP++   +   KI
Sbjct: 446 SSDSFVQYTDLGASGTRMPRTNWENMKRYSLVVPPISVSEVFSSKI 491


>gi|300718522|ref|YP_003743325.1| type I restriction-modification system, S subunit [Erwinia
           billingiae Eb661]
 gi|299064358|emb|CAX61478.1| Type I restriction-modification system, S subunit [Erwinia
           billingiae Eb661]
          Length = 576

 Score = 57.0 bits (136), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 61/109 (55%), Gaps = 4/109 (3%)

Query: 21  IPKHW---KVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST 77
           +P+ W   ++  I  + + +    +++  D   + LED+E  T K L +   S +   S+
Sbjct: 101 LPEGWEWMRLGFITNYGECDKAEPTDANADTWIVELEDIEKSTSKLLNRVKFSERPFKSS 160

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQ 125
            + F K  +LYGKL PYL K ++AD  G+C+T+ + ++   ++LP+ ++
Sbjct: 161 KNKFYKNDVLYGKLRPYLDKVLVADDSGVCTTEIIPIKGYGNILPDYIR 209


>gi|254374066|ref|ZP_04989548.1| predicted protein [Francisella novicida GA99-3548]
 gi|151571786|gb|EDN37440.1| predicted protein [Francisella novicida GA99-3548]
          Length = 417

 Score = 57.0 bits (136), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 69/146 (47%), Gaps = 15/146 (10%)

Query: 60  TGKYLPKDGNSRQSDTSTVSIFAKGQILYG----KLGPYLRKAIIADFDGICSTQFLVLQ 115
           T +++P   N+  +D S   I  KGQ  YG    + G  +  A++ D   I ST + V +
Sbjct: 33  TKEFIPSIANTVGTDMSKYKIVQKGQFAYGPVTSRNGDKISVALLEDDSAIVSTSYTVFE 92

Query: 116 PKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
             D   +LPE L  W    +  +    +  G+T     W+ + ++ +PIP + +Q   RE
Sbjct: 93  IIDKTKLLPEYLMMWFRREEFDRYARYMSHGSTREVFGWEEMCDVELPIPSIEKQ---RE 149

Query: 173 KIIAETVRIDTLITERIRFIELLKEK 198
            I+AE       IT RI+  E L +K
Sbjct: 150 -IVAEYY----AITNRIKLNEQLNQK 170


>gi|119477798|ref|ZP_01617921.1| putative specificity protein s [marine gamma proteobacterium
           HTCC2143]
 gi|119448959|gb|EAW30200.1| putative specificity protein s [marine gamma proteobacterium
           HTCC2143]
          Length = 444

 Score = 57.0 bits (136), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 84/393 (21%), Positives = 177/393 (45%), Gaps = 44/393 (11%)

Query: 55  DVESGTGKYLPKDGNSRQSDTSTVSI----FAKGQILYGKLGPYLRKAIIADFDG--ICS 108
           D+++GT   + ++  +R SD+    +     +KG I+YG+ G   R+A++ + +   +C 
Sbjct: 46  DIKNGT---IAQERIARVSDSHVSRLAMHQLSKGDIVYGRRGDIGRQALVKEAESGWLCG 102

Query: 109 TQFL--VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAE 166
           T  L   L   +V+PE L  +L   ++   I+    GATM + +   +  +P+  P    
Sbjct: 103 TGCLRITLGESEVIPEYLHLYLKMPEIIGWIQNQAIGATMPNLNTSILRRVPIHFP---S 159

Query: 167 QVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVG 226
               +  I++ +   D LI    R I +L+   + +      +   P  K     +E+  
Sbjct: 160 SKATQRNIVSLSFAYDDLIENIKRRINILESMGEEIYREWFVRFRFPGHK----AVEFKK 215

Query: 227 LVPDHWEV---KPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETY 283
            VP  W V     FF  V   + K+ ++ +++  S+ +  +  K   R  G + +  + Y
Sbjct: 216 GVPKDWVVGRASLFFEHVKGRSYKSEEISDTDDESMPF--VTLKSFNRGGGYRSDGLKLY 273

Query: 284 -------QIVDPGEIVFRFIDL-QNDKRSLRSAQVMERG----IITSAYMAVKPHGIDST 331
                  Q+V  G++V    D+ QN +   R A+V E G    +I+   + + P  + +T
Sbjct: 274 SGKFSSSQVVHEGDVVMAVTDMTQNREVVGRVARVPEMGRRGAVISLDVIKLVPKSVSAT 333

Query: 332 YLAWLMRSYDLCKVFYAMGSGLR-QSLKFEDVKRLPVLVPP--IKEQFDITNVINVETAR 388
           YL   ++         +  +G     LK + V +  ++VP   ++E+F+   +++    +
Sbjct: 334 YLYSYIKYSGFSHFIKSFANGANVLHLKPDLVTQQVIVVPTQGLREKFEA--IVDPIHEQ 391

Query: 389 IDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           + +L ++I+     L+  R S +   ++G++ +
Sbjct: 392 VGLLSKEIDN----LEATRDSLLPRLISGKLSV 420


>gi|254383777|ref|ZP_04999125.1| type I restriction-modification system specificity subunit
           [Streptomyces sp. Mg1]
 gi|194342670|gb|EDX23636.1| type I restriction-modification system specificity subunit
           [Streptomyces sp. Mg1]
          Length = 403

 Score = 56.6 bits (135), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 51/92 (55%), Gaps = 1/92 (1%)

Query: 316 ITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFE-DVKRLPVLVPPIKE 374
           +  +   ++P GID  +L +++ S         +  G+     F+ D+ RLPV VPP++E
Sbjct: 86  VNGSIAVIRPTGIDGAFLRYVLASRVTQAAINMLKGGMGVPHLFQWDINRLPVPVPPLEE 145

Query: 375 QFDITNVINVETARIDVLVEKIEQSIVLLKER 406
           Q  I + ++VETARID L +   +   LL+ER
Sbjct: 146 QRRIADFLDVETARIDRLTQLRSRQAGLLEER 177



 Score = 45.8 bits (107), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 80/321 (24%), Positives = 132/321 (41%), Gaps = 27/321 (8%)

Query: 113 VLQPKDVLPELLQGWLLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
           V++P  +    L+ ++L+  VTQ  I  +  G  + H     I  +P+P+PPL EQ  I 
Sbjct: 92  VIRPTGIDGAFLR-YVLASRVTQAAINMLKGGMGVPHLFQWDINRLPVPVPPLEEQRRIA 150

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH 231
           + +  ET RID L   R R   LL+E+           GL  D   +++  E   L    
Sbjct: 151 DFLDVETARIDRLTQLRSRQAGLLEER----------FGLALDKAFENATYEPTRL-KYL 199

Query: 232 WEVKPFFA-LVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
             VKP +  LV + +    + I  N L L        L      L  +   T  +  PG+
Sbjct: 200 LAVKPRYGVLVPQYSDSGVRFIRVNDL-LDLAGRADSLAKIPDELSSQYART--VTRPGD 256

Query: 291 IVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLA-WLMRSYDLCKVFYAM 349
           ++   +     + ++   Q+    +  +       H +    LA WL     L +     
Sbjct: 257 VLLSVVGTMG-RSAVVPPQLAGANVARAVASLRTRHEVSPELLATWLTTPSFLRQASDVT 315

Query: 350 GSGLRQ-SLKFEDVKRLPVLVPPIKEQFD----ITNVINVETARIDVLVEKIEQSIVLLK 404
           GS   Q +L  ED+    +  P  +   D    +T+ I      +  ++E +++ +  L 
Sbjct: 316 GSDTAQPTLGMEDLSNFRLSWPVDERGRDELLLVTSTIRRHQRELTGVLE-VQRRV--LT 372

Query: 405 ERRSSFIAAAVTGQIDLRGES 425
           ERR + I AAVTGQ D+   S
Sbjct: 373 ERRQALITAAVTGQFDVSTAS 393


>gi|30065580|ref|NP_839751.1| hypothetical protein S4635 [Shigella flexneri 2a str. 2457T]
 gi|30043844|gb|AAP19563.1| hypothetical protein S4635 [Shigella flexneri 2a str. 2457T]
 gi|313646315|gb|EFS10777.1| type I restriction enzyme EcoAI specificity [Shigella flexneri 2a
           str. 2457T]
          Length = 551

 Score = 56.6 bits (135), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 10/195 (5%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIY-IGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           +P+ W+   I     + +   S      +Y +  + +E GTG+ + K            S
Sbjct: 364 LPEGWEWCRIGNIVNIKSELVSPKDYLNLYQVAPDIIEKGTGRVISKRTVKESGVKGPNS 423

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL--PELLQGWLLSIDVTQRI 137
            F KGQI+Y K+ P L K  +A+++G+CS     + P D    P  L  ++LSI    ++
Sbjct: 424 RFYKGQIVYSKIRPSLSKVFLAEYNGLCSAD---MYPLDCYINPNYLLKYILSIPFLMQV 480

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKE 197
           +       M   +     NI + IPP  EQ  I +KI +    I+ +    I +I +  +
Sbjct: 481 KKAENRIKMPKLNSDSFYNIIVAIPPYNEQQAIFDKINS----IEAVCNGLISYIGIYHK 536

Query: 198 KKQALVSYIVTKGLN 212
            +  L   +    +N
Sbjct: 537 TQLHLADALTDAAIN 551


>gi|291534513|emb|CBL07625.1| Type I restriction modification DNA specificity domain [Roseburia
           intestinalis M50/1]
          Length = 199

 Score = 56.6 bits (135), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 31/106 (29%), Positives = 55/106 (51%), Gaps = 2/106 (1%)

Query: 73  SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ--PKDVLPELLQGWLLS 130
           ++ +   +F KG +L+G+   YL+KA +A FDGICS    V++  P  +LPELL   + +
Sbjct: 46  AENTFTKMFRKGDVLFGRRRAYLKKAAVAPFDGICSGDITVIEADPDKILPELLPFIIQN 105

Query: 131 IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
            D+         G+      W+ + N  + +P + +Q  + E + A
Sbjct: 106 DDLFDFAVGKSAGSLSPRVKWEHLKNYELELPDMNKQKELAELLWA 151


>gi|24115563|ref|NP_710073.1| hypothetical protein SF4364 [Shigella flexneri 2a str. 301]
 gi|110808124|ref|YP_691644.1| hypothetical protein SFV_4365 [Shigella flexneri 5 str. 8401]
 gi|24054894|gb|AAN45780.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|110617672|gb|ABF06339.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|281603673|gb|ADA76657.1| hypothetical protein SFxv_4757 [Shigella flexneri 2002017]
          Length = 553

 Score = 56.6 bits (135), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 75/169 (44%), Gaps = 6/169 (3%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIY-IGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           +P+ W+   I     + +   S      +Y +  + +E GTG+ + K            S
Sbjct: 366 LPEGWEWCRIGNIVNIKSELVSPKDYLNLYQVAPDIIEKGTGRVISKRTVKESGVKGPNS 425

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVL--PELLQGWLLSIDVTQRI 137
            F KGQI+Y K+ P L K  +A+++G+CS     + P D    P  L  ++LSI    ++
Sbjct: 426 RFYKGQIVYSKIRPSLSKVFLAEYNGLCSAD---MYPLDCYINPNYLLKYILSIPFLMQV 482

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
           +       M   +     NI + IPP  EQ  I +KI +     + LI+
Sbjct: 483 KKAENRIKMPKLNSDSFYNIIVAIPPYNEQQAIFDKINSIEAVCNGLIS 531


>gi|315169212|gb|EFU13229.1| type I restriction modification DNA specificity domain protein
           [Enterococcus faecalis TX1341]
          Length = 411

 Score = 56.2 bits (134), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 48/152 (31%), Positives = 70/152 (46%), Gaps = 8/152 (5%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
            ED+ +G G+ L KD  S++ D      F    ILYGKL PYL+  + A F G+    F 
Sbjct: 46  FEDIVAGEGR-LNKDV-SQKFDNRKGIEFLPNDILYGKLRPYLKNWLKATFTGVALGDFW 103

Query: 113 VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP-PLAEQVLIR 171
           V + K+   + +   L+  D  Q+      G  M  +DWK +      +P  L EQ    
Sbjct: 104 VFRVKNSDSDFIYS-LIQADRYQKAANDTSGTKMPRSDWKKVSGTVFYVPNDLKEQ---- 158

Query: 172 EKIIAETVRIDTLITERIRFIELLKEKKQALV 203
           +KI     +ID  IT   R ++ LK  K A +
Sbjct: 159 QKIGTLFKQIDDAITLHQRKLDQLKNLKNAFL 190


>gi|296535588|ref|ZP_06897769.1| specificity determinant for HsdM and hsdR [Roseomonas cervicalis
           ATCC 49957]
 gi|296264104|gb|EFH10548.1| specificity determinant for HsdM and hsdR [Roseomonas cervicalis
           ATCC 49957]
          Length = 480

 Score = 56.2 bits (134), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 77/181 (42%), Gaps = 8/181 (4%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT-STVSIFAKGQILYGKLGPYLRKAII 100
           +++  ++ ++GLE +       L   G  R  D  S  S F  G +LY ++ PYL K   
Sbjct: 31  ADAKSNLPFVGLEHIAP---HALRPHGFGRFGDMRSAASPFTPGDVLYARMRPYLNKVWH 87

Query: 101 ADFDGICSTQFLVLQPKD--VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIP 158
           AD +G+ S +FLVL P+   V P+ L   L      +       G      +W  I   P
Sbjct: 88  ADREGVASAEFLVL-PRSGRVHPDFLALLLHHRPFVEFARHASSG-DRPRVEWADISKYP 145

Query: 159 MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
           + +PP AEQ  I   + A    ++       R  E L + + +L+    T  L  D +  
Sbjct: 146 IALPPRAEQDRIVTAVNALFDEVEAGEASLARAREGLTQFRTSLLHAACTGALTADWRTA 205

Query: 219 D 219
           +
Sbjct: 206 N 206



 Score = 40.0 bits (92), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 23/107 (21%), Positives = 50/107 (46%), Gaps = 1/107 (0%)

Query: 314 GIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPI 372
           G+ ++ ++ +   G +   +LA L+      +      SG R  +++ D+ + P+ +PP 
Sbjct: 92  GVASAEFLVLPRSGRVHPDFLALLLHHRPFVEFARHASSGDRPRVEWADISKYPIALPPR 151

Query: 373 KEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
            EQ  I   +N     ++     + ++   L + R+S + AA TG +
Sbjct: 152 AEQDRIVTAVNALFDEVEAGEASLARAREGLTQFRTSLLHAACTGAL 198


>gi|16767768|ref|NP_463383.1| type I restriction enzyme specificity protein [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|167991322|ref|ZP_02572421.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168243978|ref|ZP_02668910.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|194449649|ref|YP_002048547.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|197262037|ref|ZP_03162111.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|135211|sp|P06187|T1S_SALTY RecName: Full=Type-1 restriction enzyme StySJI specificity protein;
           Short=S.StySJI; AltName: Full=Type I restriction enzyme
           StySJI specificity protein; Short=S protein
 gi|47739|emb|CAA68580.1| S polypeptide [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|16423091|gb|AAL23342.1| specificity determinant for hsdM and hsdR [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|194407953|gb|ACF68172.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|197240292|gb|EDY22912.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|205330268|gb|EDZ17032.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205337035|gb|EDZ23799.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|261249609|emb|CBG27479.1| type I restriction enzyme [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267996882|gb|ACY91767.1| type I restriction enzyme specificity protein [Salmonella enterica
           subsp. enterica serovar Typhimurium str. 14028S]
 gi|301161007|emb|CBW20544.1| type I restriction enzyme [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312915621|dbj|BAJ39595.1| type I restriction enzyme StySJI specificity protein [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           T000240]
 gi|323132866|gb|ADX20296.1| type I restriction enzyme specificity protein [Salmonella enterica
           subsp. enterica serovar Typhimurium str. 4/74]
 gi|332991333|gb|AEF10316.1| type I restriction enzyme specificity protein [Salmonella enterica
           subsp. enterica serovar Typhimurium str. UK-1]
          Length = 469

 Score = 56.2 bits (134), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 95/435 (21%), Positives = 180/435 (41%), Gaps = 45/435 (10%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTV 78
           G +P+ W    I     LN     +   D+ ++ +  V +    YL K  N      S V
Sbjct: 4   GKLPEGWATSTINEMCNLNPKLKLDDDLDVGFMPMAGVPT---TYLGK-CNFETKKWSEV 59

Query: 79  ----SIFAKGQILYGKLGPYL---RKAIIADFD---GICSTQFLVLQPKDVLPELLQGWL 128
               + F    +++ K+ P     +  +I +F    G  ST++ VL+  + L  +   WL
Sbjct: 60  KKGFTQFQNDDVIFAKITPCFENGKAVVIKEFPNGYGAGSTEYYVLRSINGL--INPHWL 117

Query: 129 LSIDVTQRI---EAICEGATMSH--ADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDT 183
            ++  T+      A+    ++ H     + + N  +P+PPLAEQ +I EK+     ++D+
Sbjct: 118 FALVKTKDFLTNGALNMSGSVGHKRVTKEFLENYGVPVPPLAEQKVIAEKLDTLLAQVDS 177

Query: 184 LITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG--IEWVGLVPDHWEVKPF--FA 239
                 +  ++LK  +Q+++   V   L  ++  K+     E    +P  W++     FA
Sbjct: 178 TKARLEQIPQILKRFRQSVIVAAVNGQLTKELHKKNKFKLTELNISIPSLWKISEIGQFA 237

Query: 240 LVTELNR--KNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
            V    R  K   LI  N     Y   I+  + +N  + PE  + Y      + + R+  
Sbjct: 238 DVKGGKRLPKGESLIAENT-GFPY---IRAGQLKNGTVLPEG-QLYLEEYIQKSISRYTV 292

Query: 298 LQNDKR-SLRSAQVMERGIITSAYMAVK-----------PHGIDSTYLA-WLMRSYDLCK 344
              D   ++  A + + GII   Y                  I + +L+ WL  SY    
Sbjct: 293 SSGDLYITIVGACIGDAGIIPDVYNNANLTENAAKICNLNENIFNRFLSLWLRSSYLQDI 352

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           +   + SG +  L    +K LP+++PP++EQ +I   +    A  D + +++  ++  + 
Sbjct: 353 INSEIKSGAQGKLALARIKSLPLILPPLQEQHEIVRRVEQLFAYADTIEKQVNNALTRVN 412

Query: 405 ERRSSFIAAAVTGQI 419
               S +A A  G++
Sbjct: 413 SLTQSILAKAFRGEL 427


>gi|326201156|ref|ZP_08191028.1| restriction modification system DNA specificity domain [Clostridium
           papyrosolvens DSM 2782]
 gi|325988724|gb|EGD49548.1| restriction modification system DNA specificity domain [Clostridium
           papyrosolvens DSM 2782]
          Length = 397

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 104/433 (24%), Positives = 174/433 (40%), Gaps = 82/433 (18%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIG---------------LEDVESGTGK 62
           +G IP+ W+V  I+    + TG T   GK   Y+                + D +     
Sbjct: 11  LGEIPQEWEVRKIEDLYSVLTGATPLRGKQEYYLNGNVAWVKTLDLNDRYIYDTQEKITD 70

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII----ADFDGICSTQFLVLQPKD 118
              K+ + +  D  TV I      +YG      R  I+    A    ICS   +    ++
Sbjct: 71  LALKETSCKVQDEGTVLI-----AMYGGFNQIGRTGILKTKAATNQAICSLPLI----EE 121

Query: 119 VLPELLQGWLL-SIDVTQRIEAIC-EGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIA 176
           + PE L  +L+ + +V + + A   +   ++  D   +    + +PPL+EQ  I +  I 
Sbjct: 122 IYPEYLNYFLIKNRNVWRNVAASTRKDPNITKGD---VEKFNIIVPPLSEQYKIAD--IL 176

Query: 177 ETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP 236
            T  ID  I +    IE  +E K+ L+  ++ KG+    + +D+ I   G +P  WEVK 
Sbjct: 177 ST--IDEQIDKTDALIEKTRELKKGLMQKLLIKGIG-HTEFRDTEI---GRIPKGWEVKK 230

Query: 237 FFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFI 296
              +V     KN K +E        G I                  Y+I+  G ++    
Sbjct: 231 LEEIVQICYGKNQKEVEIE------GGI------------------YKILGTGGVIGNTN 266

Query: 297 DLQNDKRSL---RSAQVMERGIITSAYMAVKP---HGIDSTYLA-WL---MRSYDLCKVF 346
           D   DK S+   R   + +   I   +  V       +D  Y+A WL   +   DL K  
Sbjct: 267 DYLWDKPSVLIGRKGTIDKPMYIEEPFWTVDTLFYTKVDEGYVAKWLYYYLNKIDLKKYN 326

Query: 347 YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
            A G     SL    +  + +LVPP KEQ  I+ +++   + IDV   K  +    L+  
Sbjct: 327 EATGV---PSLSVAVLNTILILVPPFKEQQKISKILSAVDSDIDVYESKKNK----LENA 379

Query: 407 RSSFIAAAVTGQI 419
           + + +   +TG+I
Sbjct: 380 KKALMNHLLTGKI 392


>gi|254932531|ref|ZP_05265890.1| HsdS [Listeria monocytogenes HPB2262]
 gi|293584086|gb|EFF96118.1| HsdS [Listeria monocytogenes HPB2262]
          Length = 404

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/152 (28%), Positives = 65/152 (42%), Gaps = 13/152 (8%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
           +  ED+ +  G+ L KD  S + D+    +F    ILYGKL PYL+  +  DF G+    
Sbjct: 253 VEYEDIIAEEGR-LNKDI-SNKFDSRKGILFQPKNILYGKLRPYLKNWLYPDFKGVAVGD 310

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           F V +  +  P  +   L+  D  Q++     G  M  +DW  + N    IP        
Sbjct: 311 FWVFEAIEATPRFIYN-LIQSDSYQKVANDTAGTKMPRSDWTKVSNSSFFIP-------- 361

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQAL 202
             K  +E  RI T   +    I L + K Q L
Sbjct: 362 --KESSEQKRIGTFFKQLDDTIALHQRKLQKL 391


>gi|332310722|gb|EGJ23817.1| HsdS [Listeria monocytogenes str. Scott A]
          Length = 391

 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/152 (28%), Positives = 65/152 (42%), Gaps = 13/152 (8%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
           +  ED+ +  G+ L KD  S + D+    +F    ILYGKL PYL+  +  DF G+    
Sbjct: 240 VEYEDIIAEEGR-LNKDI-SNKFDSRKGILFQPKNILYGKLRPYLKNWLYPDFKGVAVGD 297

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
           F V +  +  P  +   L+  D  Q++     G  M  +DW  + N    IP        
Sbjct: 298 FWVFEAIEATPRFIYN-LIQSDSYQKVANDTAGTKMPRSDWTKVSNSSFFIP-------- 348

Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQAL 202
             K  +E  RI T   +    I L + K Q L
Sbjct: 349 --KESSEQKRIGTFFKQLDDTIALHQRKLQKL 378


>gi|149185163|ref|ZP_01863480.1| hypothetical protein ED21_18957 [Erythrobacter sp. SD-21]
 gi|148831274|gb|EDL49708.1| hypothetical protein ED21_18957 [Erythrobacter sp. SD-21]
          Length = 388

 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 75/160 (46%), Gaps = 11/160 (6%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
           I L++VE  +G+ +       +      + F    ILY KL PYL K   AD  G+ ST+
Sbjct: 215 IELDNVEGQSGRLI--GATPTKELQGARATFQTADILYCKLRPYLNKFHYADRPGLASTE 272

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICE---GATMSHADWKGIGNIPMPIPPLAEQ 167
           F VL+    + E  Q +L  +  T    A      G+ M  ADW+ +   P+P+P   EQ
Sbjct: 273 FWVLRADRDVCE--QRFLFHLIQTHEFAAEANRPTGSRMPRADWEVVQGAPLPLPSKDEQ 330

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIV 207
             +   +  +    D L    IR  ELL+ KK++L+  ++
Sbjct: 331 ANL--LLPLDAAHSDWLAE--IRRGELLQIKKRSLMQRLL 366


>gi|330721464|gb|EGG99514.1| Type I restriction-modification system2C specificity subunit S
           [gamma proteobacterium IMCC2047]
          Length = 413

 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 68/301 (22%), Positives = 132/301 (43%), Gaps = 36/301 (11%)

Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQAL 202
           G+        G+  I  P PPL EQ    +KI A    +D +I +    I+ LK+ K  +
Sbjct: 127 GSAQPQITGAGLKFIEFPAPPLPEQ----QKIAAILSSVDEVIEKTRAQIDKLKDLKTGM 182

Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLI------ESNI 256
              ++TKG+    + KDS    VG +P  W+V P   LV         ++      E  +
Sbjct: 183 RQELLTKGVG-HTEFKDSP---VGRIPVGWDVVPLEKLVKAGKNITYGIVQAGPHYEGGV 238

Query: 257 LSLSYGNIIQKLETRNMGL--KPESYETYQ--IVDPGEIVFRFIDLQNDKRSLRSAQVME 312
             +   ++  +  +RN  L   PE  E Y+   V  G+IV+        +  +   Q++ 
Sbjct: 239 PYIRVSDMTGRSLSRNGMLLTSPEIAEKYERSAVSSGDIVYAL------RGVIGHVQIVP 292

Query: 313 RGI----ITSAYMAVKPHG-IDSTYLAWLMRS--YDLCKVFYAMGSGLRQSLKFEDVKRL 365
           + +    +T     V P+  +D+ YL W M+S   +      A GS  R+ +    ++++
Sbjct: 293 KDLDGANLTQGTARVSPNELVDTRYLLWAMKSPYVEYQNDLEAKGSTFRE-VTLASLRKI 351

Query: 366 PVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGES 425
            +  P + EQ  I +++      +++ +  +E  +V L+  + + +   +TG++ +  E 
Sbjct: 352 QIATPELNEQKRIASIL----GSVELKIFAVEDKLVHLESIKKALMQDLLTGKVRVNVEQ 407

Query: 426 Q 426
           +
Sbjct: 408 K 408


>gi|293408034|ref|ZP_06651874.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291472285|gb|EFF14767.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 576

 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/193 (24%), Positives = 83/193 (43%), Gaps = 6/193 (3%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIY-IGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           +P+ W+   I     + +   S      +Y +  + +E GTG+ + K            S
Sbjct: 389 LPEGWEWCRIGNIVNIKSELVSPKDYLNLYQVAPDIIEKGTGRVISKRTVKESGVKGPNS 448

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEA 139
            F KGQI+Y K+ P L K  +A+++G+CS     L    + P  L  ++LSI    +++ 
Sbjct: 449 RFYKGQIVYSKIRPSLSKVFLAEYNGLCSADMYPLDCY-INPNYLLKYILSIPFLMQVKK 507

Query: 140 ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKK 199
                 M   +     NI + IPP  EQ  I +KI +    I+ +    I +I +  + +
Sbjct: 508 AENRIKMPKLNSDSFYNIIVAIPPYNEQQAIFDKINS----IEAVCNGLISYIGIYHKTQ 563

Query: 200 QALVSYIVTKGLN 212
             L   +    +N
Sbjct: 564 LHLADALTDAAIN 576


>gi|254993446|ref|ZP_05275636.1| hypothetical protein LmonocytoFSL_10912 [Listeria monocytogenes FSL
           J2-064]
          Length = 160

 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 52/112 (46%), Gaps = 3/112 (2%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
           +  ED+ +  G+ L KD  S + D+    +F    ILYGKL PYL+  +  DF G+    
Sbjct: 42  VEYEDIIAEEGR-LNKDI-SNKFDSRKGILFQPKNILYGKLRPYLKNWLYPDFKGVAVGD 99

Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
           F V +  +  P  +   L+  D  Q++     G  M  +DW  + N    IP
Sbjct: 100 FWVFEAIEATPRFIYN-LIQSDSYQKVANDTAGTKMPRSDWTKVSNSSFFIP 150


>gi|322369761|ref|ZP_08044324.1| restriction modification system DNA specificity domain protein
           [Haladaptatus paucihalophilus DX253]
 gi|320550679|gb|EFW92330.1| restriction modification system DNA specificity domain protein
           [Haladaptatus paucihalophilus DX253]
          Length = 437

 Score = 55.5 bits (132), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 102/240 (42%), Gaps = 31/240 (12%)

Query: 20  AIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLE--DVESGTGKYLPKDGNSRQSDTST 77
           AIP+ W  VP +   +LN            Y+ ++  D +  T +Y       R+ D  T
Sbjct: 25  AIPEEWDAVPFEEAIELNPRYDKPDNGPFNYLPMDAVDEDKQTIEYW----TEREKDDCT 80

Query: 78  VSIFAKGQILYGKLGPYLRKAIIADFDGI------CSTQFLVLQP-KDVLPELLQGWLLS 130
            + F  G  +Y K+ P      IA  +G+       ST+FLV  P K V  E    +L +
Sbjct: 81  TTWFKNGDTVYAKITPCTENGKIAFINGLETEVGSGSTEFLVFHPRKGVTDEQFVYYLSN 140

Query: 131 IDVTQRIE-AICEGATMSHADWKGI--GNIPMPIPPLAEQVLIREKIIAETVRIDTLITE 187
           +   + +  ++ EG+T        +  G + +P+P L EQ  I +        I + + E
Sbjct: 141 LPEFRSVTISLMEGSTGRQRVPSDVFKGGLQIPLPSLPEQRRIAD--------ILSTVDE 192

Query: 188 RIRFIELLKEKKQALVSYI----VTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTE 243
           RI+  +++ EK   L+S +     T G + D   ++ G   +   P  W++ P     T+
Sbjct: 193 RIQQTDVIIEKTNELLSGVQKDLFTTGYSDD---REVGTRRLIEAPLDWDIAPLSEFTTD 249


>gi|124008338|ref|ZP_01693033.1| type I restriction-modification system specificity subunit
           [Microscilla marina ATCC 23134]
 gi|123986127|gb|EAY25963.1| type I restriction-modification system specificity subunit
           [Microscilla marina ATCC 23134]
          Length = 424

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 94/418 (22%), Positives = 174/418 (41%), Gaps = 50/418 (11%)

Query: 10  YKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKD--------IIYIGLEDVESGTG 61
           YKDS    +G IP+ W+VV +    K++ G T    K         I ++   D+ +   
Sbjct: 6   YKDSP---LGEIPEDWEVVKLGDIAKVSAGGTPLRSKQEEYFTNGHIPWVKTLDLNNSII 62

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQIL---YGKLGPYLRKAIIA-DFDGICSTQFLVLQPK 117
           +   +   S     ++ ++  K  +L   YG      R  ++  +     +   L ++  
Sbjct: 63  EDTEEKITSLALKETSCNLLPKNTVLVAMYGGFNQIGRTGLLKIEATTNQAISALNIKSD 122

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHAD----WKGIGNIPMPIPPLAEQVLIREK 173
           ++ PE +  WL       ++E   + A  S  D     K + + P+ IPPLAEQ  I + 
Sbjct: 123 NIYPEFILAWL-----NAKVEVWKKFAASSRKDPNITKKDVEHFPIVIPPLAEQQEIADI 177

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +     +I T I ER+   + L   K+ L+  + T+GL      K S +   G +P+ WE
Sbjct: 178 LSTVDEKIAT-IDERLAHTQQL---KKGLMQRLFTRGLG-HTSFKASPL---GEIPESWE 229

Query: 234 VKPFFALV------TELNRKNTKLIESN----ILSLSYGN-IIQKLETRNMGLKPESYET 282
           V     +       T L  K  +   +     + +L   N II+  E +   L  +    
Sbjct: 230 VVKLGDIAKVSAGGTPLRSKQEEYFTNGHIPWVKTLDLNNSIIEDTEEKITSLALKETSC 289

Query: 283 YQIVDPGEIVFRFIDLQNDKRS--LRSAQVMERGIITSAYMAVKPHGIDSTY-LAWLMRS 339
             +     +V  +       R+  L+      + I   + + +K   I   + LAWL   
Sbjct: 290 NLLPKNTVLVAMYGGFNQIGRTGLLKIEATTNQAI---SALNIKSDNIYPEFILAWLNAK 346

Query: 340 YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            ++ K F A  S    ++  +DV+  P+++PP+ EQ +I +++     ++++L EK E
Sbjct: 347 VEVWKKF-AASSRKDPNITKKDVEHFPIVIPPLAEQQEIADILGGVDEKLELLAEKKE 403



 Score = 36.6 bits (83), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 333 LAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVL 392
           LAWL    ++ K F A  S    ++  +DV+  P+++PP+ EQ +I ++++    +I  +
Sbjct: 130 LAWLNAKVEVWKKF-AASSRKDPNITKKDVEHFPIVIPPLAEQQEIADILSTVDEKIATI 188

Query: 393 VEKIEQSIVLLK 404
            E++  +  L K
Sbjct: 189 DERLAHTQQLKK 200


>gi|167461699|ref|ZP_02326788.1| putative type I restriction enzyme specificity subunit
           [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322384020|ref|ZP_08057748.1| hypothetical protein PL1_2076 [Paenibacillus larvae subsp. larvae
           B-3650]
 gi|321151387|gb|EFX44576.1| hypothetical protein PL1_2076 [Paenibacillus larvae subsp. larvae
           B-3650]
          Length = 410

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 82/359 (22%), Positives = 170/359 (47%), Gaps = 41/359 (11%)

Query: 79  SIFAKGQILYGKLGPYLR-------KAIIADFDGICSTQFLVLQPKDVLPELLQGWLL-S 130
           + F +  IL+ K+ P +        K ++  F G  ST+F VL+P +++      +LL S
Sbjct: 27  TYFQENDILFAKITPCMENGNTVIAKGMLNKF-GFGSTEFYVLRPSNIVEGRFIYYLLRS 85

Query: 131 IDVTQRIEAICEGAT-MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERI 189
               +  +A+  GA        K + + P+ +PPL EQ  I +KI +   ++D  I +R+
Sbjct: 86  EKFRKEAKAVMSGAVGQQRVPKKFLIDYPLCLPPLNEQKRIADKIESLFAKMD--IAKRL 143

Query: 190 RFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF------FALVTE 243
             I+  KE  +   + I+ K    ++  K+  +  V ++P+     P+       + V +
Sbjct: 144 --IDEAKESFELRRAAILDKAFRGEL-TKEWRLSQVEILPNLETKIPYGWKHVILSDVVQ 200

Query: 244 LNRKNTKLI----ESNILSLSYGNI------IQKLETRNMGLKPESYETYQIVDPGEIVF 293
           +N + TKL     E     +  G +      I++ E ++  +  + Y TY   +  +I+F
Sbjct: 201 VNPRRTKLQHISDEQECTFVPMGAVSEISGTIEEPEVKSFVIVKKGY-TY--FEENDIIF 257

Query: 294 RFID--LQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRS--YDLCKVFYA 348
             I   ++N K +L S  +   G  ++ +  ++    I++ Y+ +L+RS  +      + 
Sbjct: 258 AKITPCMENGKTALASKLINGFGFGSTEFHVIRAKQHINNKYIYFLLRSSKFRYEAKMHM 317

Query: 349 MGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID--VLVEKIEQSIVLLKE 405
            G+  +Q +    ++     +PP++EQ  I +++     + D  +++E++E+SI LLK+
Sbjct: 318 TGAVGQQRVPKSFLENYKFQLPPVEEQAKIVDLLEKIYDKEDKALVIEQLEESIKLLKQ 376


>gi|237653812|ref|YP_002890126.1| type I restriction-modification system, endonuclease S subunit
           [Thauera sp. MZ1T]
 gi|237625059|gb|ACR01749.1| type I restriction-modification system, endonuclease S subunit
           [Thauera sp. MZ1T]
          Length = 141

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/110 (35%), Positives = 57/110 (51%), Gaps = 5/110 (4%)

Query: 23  KHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFA 82
           K W+   I           SESG +  Y+GLE ++S + K   +   S     +T  +F 
Sbjct: 11  KVWRFDQIATNVNERVDNPSESGMEH-YVGLEHLDSDSLKI--RRWGSPDDVEATKLVFR 67

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLVL--QPKDVLPELLQGWLLS 130
           KG I++G+   Y RK  +A+FDGICS   +VL  +P  VLPE L  ++ S
Sbjct: 68  KGDIIFGRRRAYQRKLGVAEFDGICSAHAMVLRAKPDVVLPEFLPFFMQS 117


>gi|240172538|ref|ZP_04751197.1| type I restriction-modification system specificity determinant
           [Mycobacterium kansasii ATCC 12478]
          Length = 66

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/55 (47%), Positives = 38/55 (69%)

Query: 367 VLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           V+VPP  EQ  I N ++ +T ++D L+ + E+ I L +ERRS+ I A VTGQID+
Sbjct: 7   VVVPPADEQASILNYLDQQTTKVDTLIAESERFIELARERRSALITAVVTGQIDV 61



 Score = 46.2 bits (108), Expect = 0.010,   Method: Composition-based stats.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
           +PP  EQ  I   +  +T ++DTLI E  RFIEL +E++ AL++ +VT
Sbjct: 9   VPPADEQASILNYLDQQTTKVDTLIAESERFIELARERRSALITAVVT 56


>gi|218708015|ref|YP_002415534.1| EcoKI restriction-modification system protein HsdS [Escherichia
           coli UMN026]
 gi|293403006|ref|ZP_06647103.1| type-1 restriction enzyme EcoKI specificity protein [Escherichia
           coli FVEC1412]
 gi|298378533|ref|ZP_06988417.1| type-1 restriction enzyme EcoKI specificity protein [Escherichia
           coli FVEC1302]
 gi|300899292|ref|ZP_07117558.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli MS 198-1]
 gi|301646864|ref|ZP_07246710.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli MS 146-1]
 gi|218435112|emb|CAR16068.1| specificity determinant for hsdM and hsdR [Escherichia coli UMN026]
 gi|291429921|gb|EFF02935.1| type-1 restriction enzyme EcoKI specificity protein [Escherichia
           coli FVEC1412]
 gi|298280867|gb|EFI22368.1| type-1 restriction enzyme EcoKI specificity protein [Escherichia
           coli FVEC1302]
 gi|300357071|gb|EFJ72941.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli MS 198-1]
 gi|301074917|gb|EFK89723.1| type I restriction modification DNA specificity domain protein
           [Escherichia coli MS 146-1]
          Length = 464

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 90/438 (20%), Positives = 180/438 (41%), Gaps = 56/438 (12%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY--------IGLEDVESG---------TG 61
           G +P+ W + P+   T L  G T +  + I Y        I   ++++G           
Sbjct: 4   GKLPEGWVIAPVSTVTTLIRGVTYKKEQAINYLKDDYLPLIRANNIQNGKFDTTDLVFVP 63

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVL 120
           K L K+      +   +++ +  + + GK   +        F   C     VL+P K + 
Sbjct: 64  KNLVKENQKISPEDIVIAMSSGSKSVVGK-SAHQHLPFECSFGAFCG----VLRPEKLIF 118

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
              +  +  S     +I ++  GA +++        I +PIPPLAEQ +I EK+     +
Sbjct: 119 SGFIAHFTKSSLYRNKISSLSAGANINNIKPASFDLINIPIPPLAEQKIIAEKLDTLLAQ 178

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP--FF 238
           +D+      +  ++LK  +QA++   V   L           +W    P H   K   F 
Sbjct: 179 VDSTKARFEQIPQILKRFRQAVLGGAVNGKLTE---------KWRNFEPQHSVFKKLNFE 229

Query: 239 ALVTEL-NRKNTKLIESN-------ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
           +++TEL N  ++K  ES        I S+  G++ Q  + R +         +++ D G+
Sbjct: 230 SILTELRNGLSSKPNESGVGHPILRISSVRAGHVDQN-DIRFLECSESELNRHKLQD-GD 287

Query: 291 IVF-------RFIDLQNDKRSLRSAQVMERGIITSAYMA--VKPHGIDSTYLAWLMRSYD 341
           ++F        F+ +    + L+   ++    +  A +     P  I+  + +   R+  
Sbjct: 288 LLFTRYNGSLEFVGVCGLLKKLQHQNLLYPDKLIRARLTKDALPEYIEIFFSSPSARNAM 347

Query: 342 LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
           +  V    G   ++ +  +D+K   VL+PP+KEQ +I   +    A  D + +++  ++ 
Sbjct: 348 MNCVKTTSG---QKGISGKDIKSQVVLLPPVKEQAEIVRRVEQLFAYADTIEKQVNNALA 404

Query: 402 LLKERRSSFIAAAVTGQI 419
            +     S +A A  G++
Sbjct: 405 RVNNLTQSILAKAFRGEL 422


>gi|300070274|gb|ADJ59674.1| specificity determinant HsdS [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 415

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 83/358 (23%), Positives = 152/358 (42%), Gaps = 60/358 (16%)

Query: 83  KGQILYGKLG-PYLRKAIIADFDGICSTQFLVLQP--KDVLPELLQGWLLSIDVTQRIEA 139
           +G I+  + G P L   +  + +G  +   L+ +P  + +L E +  ++ S    ++I  
Sbjct: 84  QGDIITARTGYPGLSAVVPKELEGAQTFTTLITRPISEMILSEYISIFINSPYGMKQISG 143

Query: 140 ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKK 199
           +  G    + +   + N+ +P+P L EQ    +KI    +++D  I    R I+LLKE+K
Sbjct: 144 MEAGGAQKNVNAGIVQNLLIPLPSLDEQ----KKISNFILKLDDTIALNQRKIDLLKEQK 199

Query: 200 QALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN---------RKNTK 250
           +  +  +      P    K   + + G V D WE +    L+T  N          K TK
Sbjct: 200 KGYLQKMF-----PKNGAKVPELRFAGFV-DDWEQRKLSDLMTFSNGINAPKENYGKGTK 253

Query: 251 LIES----NILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLR 306
           +I      N L + Y NI+  +         +  E    V+ G+++F           +R
Sbjct: 254 MISVMDILNPLPIKYDNILNSVSV------DKKIEDKNKVENGDLIF-----------VR 296

Query: 307 SAQVMERGIITSAY----------MAVKPHGIDS--TYLAWLMRSY-DLCKVFYAMGSGL 353
           S++++E      AY           A++   I S   Y   L  +Y +  ++    G   
Sbjct: 297 SSEIVEEVGWAKAYKEARYALYSGFAIRGKRISSYNAYFIELTLNYANRKEIKRRAGGST 356

Query: 354 RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
           R ++  E +  L VL P I EQ    N I++   +ID  +   ++ + LLKE++  F+
Sbjct: 357 RFNVSQEILNSLTVLTPSISEQ----NQIDLFFTKIDDTITLHQRKLDLLKEQKKGFL 410


>gi|254448613|ref|ZP_05062072.1| type I restriction-modification system, endonuclease S subunit
           [gamma proteobacterium HTCC5015]
 gi|198261802|gb|EDY86088.1| type I restriction-modification system, endonuclease S subunit
           [gamma proteobacterium HTCC5015]
          Length = 379

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 77/173 (44%), Gaps = 19/173 (10%)

Query: 49  IYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI-FAKGQILYGKLGPYLRKAIIADFDGIC 107
           IY+GLE +E    ++L  +      D     + F  G I++GK   Y RKA +A+F GIC
Sbjct: 38  IYVGLEHIEP---RHLRVNRFGSPGDVIGQKLKFNAGDIIFGKRRAYQRKAAVANFSGIC 94

Query: 108 STQFLVLQPKD--VLPELLQGWLLSIDVTQRIE-AICEGATMSHADWKGIGNIPMPIPP- 163
           S   +VL+  +  + P  L   L+  DV       I EG+      WK +     P+PP 
Sbjct: 95  SAHAMVLRENNEFIFPGFLI-HLMHTDVFMNTAIRISEGSLSPTIKWKILAEQKFPVPPK 153

Query: 164 ---------LAEQVLIREKIIAETVRIDTLITE-RIRFIELLKEKKQALVSYI 206
                    L +   I   I A T  ++TL+   + + + +  + KQA +  I
Sbjct: 154 NIQSTLLDSLTKIEEIESSIFAVTSSLNTLLASYKSKHMPIRAKAKQAKIEKI 206


>gi|317132749|ref|YP_004092063.1| restriction modification system DNA specificity subunit
           [Ethanoligenens harbinense YUAN-3]
 gi|315470728|gb|ADU27332.1| restriction modification system DNA specificity subunit
           [Ethanoligenens harbinense YUAN-3]
          Length = 462

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 91/453 (20%), Positives = 175/453 (38%), Gaps = 63/453 (13%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPK 66
           Y    ++   W+  IP HW++  I         +T  S KD  Y  L   + G    LP+
Sbjct: 4   YTDVINTDAAWLPQIPAHWQLQKIDAL--FTERKTKVSDKD--YAPLSVTKKGI---LPQ 56

Query: 67  -DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK-----DVL 120
            +  ++ +D+    +   G  +            ++  DG  S   LVL P+     D +
Sbjct: 57  LEHAAKSNDSDNRKLVKAGDFVINSRSDRKGSCGVSKLDGSVSLINLVLTPRSKLNNDYV 116

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
             LL+ +  S +  +    I   A +    +  +  I +P+PP AEQ  I   +  +   
Sbjct: 117 HYLLRNYRFSEEYYRNGRGIV--ADLWTTRYSEMRTILLPVPPRAEQDQIVRFLDWKVSE 174

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           I+ LI  R + I+   + K  +++  VT GL  + ++  +   +  ++P  W +     +
Sbjct: 175 INKLIGIRRKEIQEFNQLKNTVITKTVTTGLKRE-ELCGTDNSYYRMIPKGWRITKTLRV 233

Query: 241 ----VTELNRKNTKLIESNI-----LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEI 291
               +T+      +L E  I      ++S GN           +  + YE        E 
Sbjct: 234 LSQPLTDGPHTTPQLYEEGIPFVSAEAVSCGNGKIDFNHIRGFISQDFYE--------EC 285

Query: 292 VFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK------- 344
             +++   +D   ++S     R  I            D  +  W   +   C        
Sbjct: 286 CKKYVPKIDDIYMIKSGATTGRVSIVDT---------DRIFTIWSPLAVFRCNQEVMLPR 336

Query: 345 -VFYAMGS-------------GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARID 390
            +FYA+ +             G +Q++    +++L +  P + EQ  I   ++ +   +D
Sbjct: 337 FLFYALQALPYQQQVQDGWSYGTQQNIGMRVLEQLKLAYPDVTEQEKIACYLDDKCDMLD 396

Query: 391 VLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
             ++  E  I  L+E +S+ I+  VTG+ID+R 
Sbjct: 397 KAIQLAESKIKALQELKSTIISDVVTGKIDVRN 429


>gi|297618847|ref|YP_003706952.1| restriction modification system DNA specificity domain-containing
           protein [Methanococcus voltae A3]
 gi|297377824|gb|ADI35979.1| restriction modification system DNA specificity domain protein
           [Methanococcus voltae A3]
          Length = 412

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 70/292 (23%), Positives = 130/292 (44%), Gaps = 35/292 (11%)

Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQAL 202
           G+T+ +   K + N+ +P+PPL EQ  I E +      I+TL        E L  KK+  
Sbjct: 143 GSTIKNLSLKSLRNLCIPLPPLKEQQKIAEILTKWDNHIETL--------ENLISKKEEY 194

Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFF---ALVTELNRKNTKL--IESNIL 257
              ++   L   V+      EW  +     E+  F     L  E   KN K   I    L
Sbjct: 195 KKGLMQNLLTGKVRFPGFNEEWKEV--KLGEICKFLKGNGLSKEKLNKNGKFKCILYGEL 252

Query: 258 SLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIIT 317
             +Y  +I+++ ++    +    E   I+ P       IDL N      +  + E  +I 
Sbjct: 253 YTTYSEVIKEVLSKTDFKEKIHSEKGDILIPASTTTTGIDLAN------ATAINEENVIL 306

Query: 318 SAYMAV----KPHGIDSTYLAWLM---RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVP 370
              + +      +  ++ +LA+ +   + Y+L K  YA G+ +   L  +D+K + + +P
Sbjct: 307 GGDINILRKKYENKYNNEFLAYYLTYGKKYELAK--YAQGTTIVH-LYGKDIKNMKIQLP 363

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
            ++EQ  I  V++++   I++L EK+E    LLK ++   +   +TG+I ++
Sbjct: 364 TLEEQEQIAEVLSLQDKEIEILKEKLE----LLKMQKKGLMQKLLTGEIRVK 411


>gi|222823384|ref|YP_002574958.1| type I restriction-modification system, S subunit [Campylobacter
           lari RM2100]
 gi|222538606|gb|ACM63707.1| type I restriction-modification system, S subunit [Campylobacter
           lari RM2100]
          Length = 390

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 101/418 (24%), Positives = 166/418 (39%), Gaps = 50/418 (11%)

Query: 23  KHWKVVPIKRFTK-LNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIF 81
           K+WK+  I    + LN  R   S KD I          +G Y P  G S   D     IF
Sbjct: 2   KYWKISIIDNTCEILNNKRVPISQKDRI----------SGIY-PYYGASGIVDYIDKYIF 50

Query: 82  AKGQILYG----KLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRI 137
            +  +L G    K G +   A IA      +    +L+P + +  L+  +L+       +
Sbjct: 51  DEELVLIGEDGAKWGAFENSAFIASGKYWVNNHAHILKPNNEI--LINKFLVYFLNYSNL 108

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKE 197
           E    GAT+   + + +  I + +PPL EQ    E+I+         I E I+ +E    
Sbjct: 109 EKYITGATVKKLNQQKLKQIEILLPPLKEQ----ERIVGILDESFANIDESIKILEQDLL 164

Query: 198 KKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF--FALVTELNRKNTKLIESN 255
               L+   + K  NP   +KD+  E   L P  WE K       +T+   K    IE+ 
Sbjct: 165 NLDELMQSALQKTFNP---LKDNAKENYQL-PQDWEWKSLGEICFITDGTHKTPNYIETG 220

Query: 256 ILSLSYGNIIQ-----------KLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRS 304
           I  LS  NI +            LE  N  +K    E   I     ++ R   L    ++
Sbjct: 221 IPFLSVKNISKGFFDLSDIKYISLEEHNKLIKRAKPEFGDI-----LICRIGTL---GKA 272

Query: 305 LRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVF--YAMGSGLRQS-LKFED 361
           ++ +   E  I  S  +      I S YL + + SY +        +G G   + L    
Sbjct: 273 IKISLEFEFSIFVSLGLLKPKVKIISDYLVYFLNSYFIEGWINNNKVGGGTHTAKLNLNI 332

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
           +++ P+ +P +KEQ  I + ++  +  I  L +  +  I  L+E + S +  A  G++
Sbjct: 333 LEKCPIALPSLKEQEQIASYLDEFSLNIKDLKQNYQAQIKNLQELKKSLLDKAFKGKL 390


>gi|16132169|ref|NP_418768.1| specificity determinant for hsdM and hsdR [Escherichia coli str.
           K-12 substr. MG1655]
 gi|89111057|ref|AP_004837.1| specificity determinant for hsdM and hsdR [Escherichia coli str.
           K-12 substr. W3110]
 gi|238903436|ref|YP_002929232.1| specificity determinant for hsdM and hsdR [Escherichia coli BW2952]
 gi|331650829|ref|ZP_08351857.1| type I restriction enzyme EcoKI specificity protein (S
           protein)(S.EcoKI) [Escherichia coli M718]
 gi|135209|sp|P05719|T1SK_ECOLI RecName: Full=Type-1 restriction enzyme EcoKI specificity protein;
           Short=S.EcoKI; AltName: Full=Type I restriction enzyme
           EcoKI specificity protein; Short=S protein
 gi|322812244|pdb|2Y7C|A Chain A, Atomic Model Of The Ocr-Bound Methylase Complex From The
           Type I Restriction-Modification Enzyme Ecoki (M2s1).
           Based On Fitting Into Em Map 1534.
 gi|322812249|pdb|2Y7H|A Chain A, Atomic Model Of The Dna-Bound Methylase Complex From The
           Type I Restriction-Modification Enzyme Ecoki (M2s1).
           Based On Fitting Into Em Map 1534.
 gi|41746|emb|CAA23554.1| hsdS [Escherichia coli]
 gi|537190|gb|AAA97245.1| CG Site No. 619; alternate gene name hss [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1790807|gb|AAC77304.1| specificity determinant for hsdM and hsdR [Escherichia coli str.
           K-12 substr. MG1655]
 gi|85677088|dbj|BAE78338.1| specificity determinant for hsdM and hsdR [Escherichia coli str.
           K12 substr. W3110]
 gi|238863570|gb|ACR65568.1| specificity determinant for hsdM and hsdR [Escherichia coli BW2952]
 gi|260450839|gb|ACX41261.1| restriction modification system DNA specificity domain protein
           [Escherichia coli DH1]
 gi|315138903|dbj|BAJ46062.1| EcoKI restriction-modification system protein HsdS [Escherichia
           coli DH1]
 gi|331051283|gb|EGI23332.1| type I restriction enzyme EcoKI specificity protein (S
           protein)(S.EcoKI) [Escherichia coli M718]
          Length = 464

 Score = 54.3 bits (129), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 90/438 (20%), Positives = 180/438 (41%), Gaps = 56/438 (12%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY--------IGLEDVESG---------TG 61
           G +P+ W + P+   T L  G T +  + I Y        I   ++++G           
Sbjct: 4   GKLPEGWVIAPVSTVTTLIRGVTYKKEQAINYLKDDYLPLIRANNIQNGKFDTTDLVFVP 63

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVL 120
           K L K+      +   +++ +  + + GK   +        F   C     VL+P K + 
Sbjct: 64  KNLVKESQKISPEDIVIAMSSGSKSVVGK-SAHQHLPFECSFGAFCG----VLRPEKLIF 118

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
              +  +  S     +I ++  GA +++        I +PIPPLAEQ +I EK+     +
Sbjct: 119 SGFIAHFTKSSLYRNKISSLSAGANINNIKPASFDLINIPIPPLAEQKIIAEKLDTLLAQ 178

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKP--FF 238
           +D+      +  ++LK  +QA++   V   L           +W    P H   K   F 
Sbjct: 179 VDSTKARFEQIPQILKRFRQAVLGGAVNGKLTE---------KWRNFEPQHSVFKKLNFE 229

Query: 239 ALVTEL-NRKNTKLIESN-------ILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGE 290
           +++TEL N  ++K  ES        I S+  G++ Q  + R +         +++ D G+
Sbjct: 230 SILTELRNGLSSKPNESGVGHPILRISSVRAGHVDQN-DIRFLECSESELNRHKLQD-GD 287

Query: 291 IVF-------RFIDLQNDKRSLRSAQVMERGIITSAYMA--VKPHGIDSTYLAWLMRSYD 341
           ++F        F+ +    + L+   ++    +  A +     P  I+  + +   R+  
Sbjct: 288 LLFTRYNGSLEFVGVCGLLKKLQHQNLLYPDKLIRARLTKDALPEYIEIFFSSPSARNAM 347

Query: 342 LCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIV 401
           +  V    G   ++ +  +D+K   VL+PP+KEQ +I   +    A  D + +++  ++ 
Sbjct: 348 MNCVKTTSG---QKGISGKDIKSQVVLLPPVKEQAEIVRRVEQLFAYADTIEKQVNNALA 404

Query: 402 LLKERRSSFIAAAVTGQI 419
            +     S +A A  G++
Sbjct: 405 RVNNLTQSILAKAFRGEL 422


>gi|255690133|ref|ZP_05413808.1| putative type I restriction-modification system specificity
           determinant [Bacteroides finegoldii DSM 17565]
 gi|260624417|gb|EEX47288.1| putative type I restriction-modification system specificity
           determinant [Bacteroides finegoldii DSM 17565]
          Length = 379

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 45/97 (46%), Gaps = 3/97 (3%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSIDVTQRI 137
           F KG IL     P+LRKA + +FDGICS +  VL  KD   +L E L   + S D     
Sbjct: 59  FKKGDILLVSRNPHLRKASMVEFDGICSEKTFVLGTKDSKVLLQEFLALVMQSDDFWNYC 118

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
           E    G      +W  +      +P + EQ  I +K+
Sbjct: 119 EEHKSGGVNYFLNWSTLAKYEFYLPSIQEQKEIADKV 155


>gi|125623519|ref|YP_001032002.1| specificity determinant HsdS [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|124492327|emb|CAL97261.1| probable specificity determinant HsdS [Lactococcus lactis subsp.
           cremoris MG1363]
          Length = 416

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 83/358 (23%), Positives = 152/358 (42%), Gaps = 60/358 (16%)

Query: 83  KGQILYGKLG-PYLRKAIIADFDGICSTQFLVLQP--KDVLPELLQGWLLSIDVTQRIEA 139
           +G I+  + G P L   +  + +G  +   L+ +P  + +L E +  ++ S    ++I  
Sbjct: 85  QGDIITARTGYPGLSAVVPKELEGAQTFTTLITRPISEMILSEYISIFINSPYGMKQISG 144

Query: 140 ICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKK 199
           +  G    + +   + N+ +P+P L EQ    +KI    +++D  I    R I+LLKE+K
Sbjct: 145 MEAGGAQKNVNAGIVQNLLIPLPSLDEQ----KKISNFILKLDDTIALNQRKIDLLKEQK 200

Query: 200 QALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELN---------RKNTK 250
           +  +  +      P    K   + + G V D WE +    L+T  N          K TK
Sbjct: 201 KGYLQKMF-----PKNGAKVPELRFAGFV-DDWEQRKLSDLMTFSNGINAPKENYGKGTK 254

Query: 251 LIES----NILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLR 306
           +I      N L + Y NI+  +         +  E    V+ G+++F           +R
Sbjct: 255 MISVMDILNPLPIKYDNILNSVSV------DKKIEDKNKVENGDLIF-----------VR 297

Query: 307 SAQVMERGIITSAY----------MAVKPHGIDS--TYLAWLMRSY-DLCKVFYAMGSGL 353
           S++++E      AY           A++   I S   Y   L  +Y +  ++    G   
Sbjct: 298 SSEIVEEVGWAKAYKEARYALYSGFAIRGKRISSYNAYFIELTLNYANRKEIKRRAGGST 357

Query: 354 RQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
           R ++  E +  L VL P I EQ    N I++   +ID  +   ++ + LLKE++  F+
Sbjct: 358 RFNVSQEILNSLTVLTPSISEQ----NQIDLFFTKIDDTITLHQRKLDLLKEQKKGFL 411


>gi|15839330|ref|NP_300018.1| type I restriction-modification system specificity determinant
           [Xylella fastidiosa 9a5c]
 gi|9107979|gb|AAF85526.1|AE004080_8 type I restriction-modification system specificity determinant
           [Xylella fastidiosa 9a5c]
          Length = 412

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 54/117 (46%), Gaps = 5/117 (4%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAI 140
           F +G+IL+GKL PY  K  +A  DG+CST  +V+ P  +LP      L+ +     +E  
Sbjct: 272 FKQGEILFGKLRPYFHKVGVAPVDGVCSTDIVVIAP--ILPTWFGFVLVHVSSDAFVEYT 329

Query: 141 CEGAT---MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIEL 194
             G+T   M    W  +   P+ +P     V   + I A +  I   I E    ++L
Sbjct: 330 NAGSTGTKMPRTSWSEMAQYPVVLPHEDVAVAFNQHIQALSEEIIIKIHESRSLVQL 386


>gi|291556522|emb|CBL33639.1| Restriction endonuclease S subunits [Eubacterium siraeum V10Sc8a]
          Length = 380

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 2/97 (2%)

Query: 73  SDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ--PKDVLPELLQGWLLS 130
           SD +   +F KG +L+G+   YL+KA +A FDGICS    V++  P  +LP LL   + +
Sbjct: 46  SDNTFTKMFRKGNVLFGRRRAYLKKAAVAPFDGICSGDITVIEAIPDRILPMLLPFIIQN 105

Query: 131 IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
            ++         G+      W+ + N    +P + +Q
Sbjct: 106 DELFDFAVGKSAGSLSPRVKWEHLKNYEFELPDMDKQ 142


>gi|312114645|ref|YP_004012241.1| restriction modification system DNA specificity domain protein
           [Rhodomicrobium vannielii ATCC 17100]
 gi|311219774|gb|ADP71142.1| restriction modification system DNA specificity domain protein
           [Rhodomicrobium vannielii ATCC 17100]
          Length = 409

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 66/137 (48%), Gaps = 13/137 (9%)

Query: 42  SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIA 101
           S+   D  Y+GLE +   +   L + GN  +  TST   F  G IL+GK+ PY  K + A
Sbjct: 232 SDVSPDTPYVGLEHLPRRS-TTLGEWGNVDEV-TSTKLKFRPGDILFGKIRPYFHKVVWA 289

Query: 102 DFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEA----ICEGATMSHADWKGIGNI 157
             DGI S+  +V++ +    + L   +LS+  +    A       G  M  A+W  +   
Sbjct: 290 PCDGISSSDAIVIRARS---DDLTAIVLSVASSDAFVAHAVQTSNGTKMPRANWPVLVKY 346

Query: 158 PMPIPPLAEQVLIREKI 174
           P+P+PPL     +REK 
Sbjct: 347 PVPLPPLE----LREKF 359


>gi|189463339|ref|ZP_03012124.1| hypothetical protein BACCOP_04056 [Bacteroides coprocola DSM 17136]
 gi|189429958|gb|EDU98942.1| hypothetical protein BACCOP_04056 [Bacteroides coprocola DSM 17136]
          Length = 389

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 91/222 (40%), Gaps = 23/222 (10%)

Query: 30  IKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYG 89
           I  + + N         D   + LED+E  T K +     S++S       F KG ILY 
Sbjct: 8   ISNYGECNNVSVDSITDDDWVLELEDLEKDTAKIIQTLSRSKRSIKGVRHRFNKGDILYS 67

Query: 90  KLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWLLS---IDVTQRIEAICEGAT 145
           KL  YL K ++A   G C+T+ +      +V    L   L S   +D TQ+      G  
Sbjct: 68  KLRTYLNKVLVAPQSGYCTTEIMPFNSYCNVSSYYLNHVLRSAYFLDYTQQCGY---GVK 124

Query: 146 MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSY 205
           M         N  +P+PPLAEQ    ++I+ E     +LI      IE  KE  QA +  
Sbjct: 125 MPRLSTTDACNGMIPLPPLAEQ----KRIVKEIEHWFSLID----VIESGKEDLQATIKQ 176

Query: 206 IVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRK 247
             +K L+  +  K        LVP     +P   L+  +N K
Sbjct: 177 AKSKILDLAIHGK--------LVPQDPNDEPASELLKRINSK 210


>gi|291527172|emb|CBK92758.1| Restriction endonuclease S subunits [Eubacterium rectale M104/1]
          Length = 382

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 37/149 (24%), Positives = 64/149 (42%), Gaps = 4/149 (2%)

Query: 23  KHWKVVPIKRFTKLNTG--RTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           K W++V       ++T      +  +D  +IG++ +E  TGK +     S     S   +
Sbjct: 194 KMWQIVGFNECAVIDTNMIHNFQGYEDYPHIGIDSIEKETGKLIGYRTISEDGVVSGKYL 253

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQ-FLVLQPKDVLPELLQGWLLSID-VTQRIE 138
           F    I+Y K+ P L K  + DFDG+CS   + +L  K++      G+ L        I 
Sbjct: 254 FTPQHIIYSKIRPNLNKVALPDFDGLCSADAYPILVKKEICNREYMGYTLRNKYFLDYIL 313

Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQ 167
           A      +   + K +    +P+PP+  Q
Sbjct: 314 AFSSRTNLPKVNKKQVEGFKLPLPPMGLQ 342


>gi|121595899|ref|YP_987795.1| restriction modification system [Acidovorax sp. JS42]
 gi|120607979|gb|ABM43719.1| restriction modification system, type I [Acidovorax sp. JS42]
          Length = 396

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 3/90 (3%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSIDVTQRI 137
           F  GQ+LYG    YLRK  +ADF+GIC+    VL+P++   +LPE L   + +       
Sbjct: 68  FKPGQVLYGSRRTYLRKVAVADFEGICANTTFVLEPQNPNELLPEFLPFLMQTEAFNDFS 127

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
               +G+   + ++  +      +PP+ EQ
Sbjct: 128 VKNSKGSVNPYINFSDLAKFEFVLPPIDEQ 157


>gi|25026605|ref|NP_736659.1| hypothetical protein CE0049 [Corynebacterium efficiens YS-314]
 gi|23491884|dbj|BAC16859.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
          Length = 417

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 60/300 (20%), Positives = 129/300 (43%), Gaps = 33/300 (11%)

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLK 196
           ++A   G+T +      + ++P+P+  L +Q  I + +  ET  ID +  E  + ++L+ 
Sbjct: 123 LQAAGRGSTFTEVSASDVASLPIPVTSLDKQDWIADYLDRETAEIDAMAVELDQAMDLID 182

Query: 197 EKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLI---- 252
           E+  A V         P + ++ S I+               ++ T  +    K      
Sbjct: 183 ERFHAEVEQSFQSLDAPRMPLR-SQIQ---------------SMTTGTSVTAAKFAPAAG 226

Query: 253 ESNILSLS--YGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV 310
           E  +L+ S  +G+ + +   +++    + +E  ++  P  I    +   N    +  A  
Sbjct: 227 EPGVLATSAVFGDELNETAVKSV----DPHEYVRLTCPLRINTLLVSRMNTMNLVGKAVT 282

Query: 311 MERGIITSAYMAVKPHGID---STYLAWLMRSYDLCKVFYAMGSGLRQSLKF---EDVKR 364
           + R +    Y+  +   ++     Y+ W  RS    +    +  G   S+K    +  + 
Sbjct: 283 VGRHL-PDVYLPDRLWAVEVDVPRYIYWWTRSQSYREQIRGLAVGASDSMKTLSQQAFRS 341

Query: 365 LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           + + VPP+ +Q  +   ++    R   L  +++++  LL+ERR+  I+AAVTGQID+  +
Sbjct: 342 ITLPVPPVTQQIAVAAQLDEAAERFSALKAELQEAKGLLEERRAVLISAAVTGQIDVSAQ 401


>gi|322420368|ref|YP_004199591.1| restriction modification system DNA specificity domain-containing
           protein [Geobacter sp. M18]
 gi|320126755|gb|ADW14315.1| restriction modification system DNA specificity domain protein
           [Geobacter sp. M18]
          Length = 411

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 40/155 (25%), Positives = 69/155 (44%), Gaps = 19/155 (12%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSESGK---DIIYIGLEDVESGTGKYLPKDGNSRQSD 74
           +G IP+ W+V  +    +    R    G+      Y+GLE        ++P+   +  + 
Sbjct: 216 LGEIPQGWEVKKLGEVAE-EMRRNVPKGQIDEPTPYVGLE--------HIPRRSLALAAW 266

Query: 75  TSTVSI------FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWL 128
            +T+ +      F KG++L+GK+ PY  K  +A FDG+CS   +V++ +           
Sbjct: 267 ETTIELGSNKLEFKKGEVLFGKIRPYFHKVSVAPFDGLCSADTIVIRARRQEHYAYVVMC 326

Query: 129 LSIDV-TQRIEAICEGATMSHADWKGIGNIPMPIP 162
           +S D       A   GA M  A+W  +   P+ IP
Sbjct: 327 VSSDAFVAEASATANGAKMPRANWDVLKKHPIVIP 361



 Score = 38.9 bits (89), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 49/225 (21%), Positives = 83/225 (36%), Gaps = 23/225 (10%)

Query: 29  PIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILY 88
           P K     N        +++ Y+  E  +  T + +PK                +G IL 
Sbjct: 37  PFKMLRTTNVRNGYVDAENVRYVTEETYKKWTRRLIPK----------------RGDILL 80

Query: 89  GKLGPYLRKAIIADFDGICSTQFLVL---QPKDVLPELLQGWLLSIDVTQRIEAICEGAT 145
            +  P      I   D +   Q L      PK +  + L   LL  D+  +I+    G+T
Sbjct: 81  TREAPLGDVGKIRTDDAVFLGQRLYHFRPDPKKLDADFLLYSLLGDDLQSQIKGFGSGST 140

Query: 146 MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSY 205
           + H   + I N+   +P L     I+++I +     D LI    R I++L+   + L   
Sbjct: 141 VEHMRLEDIPNLEFNVPALP----IQQRIASILSAYDELIENSQRRIKILESMARTLYRE 196

Query: 206 IVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTK 250
                  P  + +      +G +P  WEVK    +  E+ R   K
Sbjct: 197 WFVHFRFPGHENQPRVASPLGEIPQGWEVKKLGEVAEEMRRNVPK 241


>gi|297157213|gb|ADI06925.1| restriction modification system DNA specificity subunit
           [Streptomyces bingchenggensis BCW-1]
          Length = 407

 Score = 53.9 bits (128), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 91/382 (23%), Positives = 160/382 (41%), Gaps = 50/382 (13%)

Query: 61  GKYLPKDGNSRQSDTST---VSIFAKGQILYGKLGPYLRKAIIA-DFDG-ICSTQFLVLQ 115
           GK +P   ++   +T+    V     G I++ + G   R AI+    +G +C T  + ++
Sbjct: 45  GKLVPDRNSTVSVETAARLAVHRLLSGDIIFARRGELGRSAIVTKSAEGWLCGTGSIRVR 104

Query: 116 -PKDVLPELLQGWLL-SIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
             ++ L     G+ L ++      +    G+TM + + + +  +P+ +P LA Q  I + 
Sbjct: 105 INQNRLDYRFAGYALQNLQTYSYFQKQSVGSTMENLNTEIVLGLPVALPTLANQRRIADF 164

Query: 174 IIAETVRIDTLITERIRFIELLKEK-KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
           + +ET +ID    +  R + LL EK    ++ ++    LN                 D  
Sbjct: 165 LDSETEKIDAFTHKTRRLLHLLDEKIASRILGHVGASQLN-----------------DIH 207

Query: 233 EVKPFFALVTELNRKNTKLIESN------ILSLSYGNIIQKLETRNMG--LKPESYETYQ 284
              P    V E+N+  TK++         I +   G +  +   R  G  +   +    Q
Sbjct: 208 SGSP----VREINKLLTKVVRPPIADGEVITAYRDGQVTARSLRRAEGYTVSATTEAQGQ 263

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLC 343
            VD G+IV   +D          A     G  +  Y    P +G DS +   L+R   L 
Sbjct: 264 RVDRGDIVIHGLDGFAGAIGTSEAA----GNCSPVYHVCIPRNGGDSLFYGRLLRILALS 319

Query: 344 KVFYAMGSGLRQ-SLKFED---VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQS 399
           +      +  R+ ++ F +     R+P+     KEQ +I   I  ++AR   L   +++S
Sbjct: 320 EYLGPFATSTRERAVDFRNWNLFGRIPIPDVSFKEQQEIGEWI--KSAR--PLRIAVDRS 375

Query: 400 IVLLKERRSSFIAAAVTGQIDL 421
             L  ERR + I AAVTGQID+
Sbjct: 376 NALAIERRQALITAAVTGQIDV 397


>gi|188997268|ref|YP_001931519.1| restriction modification system DNA specificity domain
           [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932335|gb|ACD66965.1| restriction modification system DNA specificity domain
           [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 425

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 100/211 (47%), Gaps = 22/211 (10%)

Query: 225 VGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGN---IIQKLETRNMGLKPESYE 281
           +GL+P+ WEV     ++ E N K       NI+ LS  +   +I++       +  ++  
Sbjct: 12  IGLIPEDWEVVRLGEILEEKNEKVKNYDFKNIVVLSITSKDGLIEQNRKFKHRVASQNIS 71

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTY---LAWLMR 338
            Y++V  GE+V+ F     ++  +      E G ++ AY   K    + TY   L +L+R
Sbjct: 72  DYKLVRKGELVYGF---PINEGVIAFLWRYEMGAVSPAYYTWKLKYPEKTYYIFLDYLLR 128

Query: 339 S---YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEK 395
           S    +L K F +     R+ +K  D K++P+ +PP++EQ  I +++    + +   +EK
Sbjct: 129 SPIILNLFKPFISNTVHRRKIIKPHDFKQIPIPLPPLEEQKAIADIL----STVQNAIEK 184

Query: 396 IEQSIVLLKERRSSFI------AAAVTGQID 420
            E+ I   K+ + S +       A V  +ID
Sbjct: 185 TEKVINATKQLKKSMMKHLFTYGAVVVDEID 215



 Score = 44.3 bits (103), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 12/91 (13%)

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLN---- 212
           IP+P+PPL EQ  I +  I  TV+     TE++  I   K+ K++++ ++ T G      
Sbjct: 158 IPIPLPPLEEQKAIAD--ILSTVQNAIEKTEKV--INATKQLKKSMMKHLFTYGAVVVDE 213

Query: 213 -PDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
              VK+K+S I   GL+P+HWEV  F  +V 
Sbjct: 214 IDKVKLKESEI---GLIPEHWEVVRFGDIVN 241



 Score = 43.9 bits (102), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 52/220 (23%), Positives = 95/220 (43%), Gaps = 40/220 (18%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTS-ESGKD------IIYIGLEDVESGTGKYLPKDGNS 70
           IG IP+HW+VV          GRTS    KD        ++ + D+++   +Y+      
Sbjct: 224 IGLIPEHWEVVRFGDIVNFKIGRTSPRKNKDYWTNGKYYWVSISDMKN---RYI------ 274

Query: 71  RQSDTSTVSIFAKGQILYGKLGP----------YLRKAIIADFDGICSTQFLVLQPKD-- 118
             + +  VS  A  +I   KL P           + +  I + D   +   + + PK+  
Sbjct: 275 -NNTSEMVSEKAHKEIFKEKLTPAGTLLMSFKLTIGRTAILNVDAYHNEAIISIYPKENK 333

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           VL E L  +L ++D +   +   +G T++ +    +  IP+P+P L EQ  I        
Sbjct: 334 VLKEFLFYYLPAVDYSNLQDKAIKGNTLNTSK---LNKIPIPLPLLDEQQKI-------- 382

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMK 218
             I T I ++I+  E  KE  Q L   ++ + +   ++++
Sbjct: 383 ANILTTIDQKIQAEEKKKEALQNLFKTLLQQLMTGKIRVR 422


>gi|158522936|ref|YP_001530806.1| restriction modification system DNA specificity subunit
           [Desulfococcus oleovorans Hxd3]
 gi|158511762|gb|ABW68729.1| restriction modification system DNA specificity domain
           [Desulfococcus oleovorans Hxd3]
          Length = 434

 Score = 53.5 bits (127), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 57/213 (26%), Positives = 95/213 (44%), Gaps = 24/213 (11%)

Query: 18  IGAIPKHWKVVPI--KRFTKLNTGRTSESGKDIIYIGLEDVES---GTGKYLPKDGNSRQ 72
            G +PK W+V P+  K    +N       G+   +I ++ +     G G YL     +++
Sbjct: 221 FGKVPKGWEVKPVGGKSLCNINPNYNFTKGEQYDFIPMDAINDDFRGLG-YLV----TKK 275

Query: 73  SDTSTVSIFAKGQILYGKLGPYLRKAIIADFD------GICSTQFLVLQPKDVLPELLQG 126
            D    + F  G IL+ K+ P      +A  +      G  ST+F++ QPK+ +      
Sbjct: 276 VDGGGYTRFRIGDILFAKITPCTENGKVALIEKMNTTVGFASTEFIIFQPKETIDNQFYF 335

Query: 127 WLLSIDVTQRIE-AICEGAT-MSHADWKGIGN-IPMPIP-PLAEQVLIREKIIAETVRID 182
           +LLS D    +  ++ EG T      WK   N I  PIP  L EQ  I +++      I+
Sbjct: 336 YLLSSDRVHNLSVSLMEGTTGRQRVPWKIFKNRILAPIPIDLDEQRNIAKRLKV----IE 391

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDV 215
            L   +   I+ LK  K++L+  ++T  +  DV
Sbjct: 392 KLNVCKYSKIQSLKNLKKSLMQNLLTGKVRVDV 424



 Score = 47.0 bits (110), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 38/134 (28%), Positives = 63/134 (47%), Gaps = 10/134 (7%)

Query: 109 TQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGAT-MSHADWKGIGNIPMPIPPLAEQ 167
           T F+   P  VLP+    WL S  + +RI ++ EG T + + D + + N+    P    +
Sbjct: 103 TGFIPKDPDTVLPKYFFYWLSSHPIQERITSVSEGTTGLGNLDIRFLRNMDFEYPKNTSE 162

Query: 168 VLIREKIIAETV-RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSG----I 222
               +K IA  + ++D +I      I+  +  K++L+  ++T  L PD   +        
Sbjct: 163 ----QKAIAGILSKVDAVIEAVENSIKAAERLKKSLMQNLLTGKLKPDGTWRSEDDFYMD 218

Query: 223 EWVGLVPDHWEVKP 236
           E  G VP  WEVKP
Sbjct: 219 EKFGKVPKGWEVKP 232


>gi|289664155|ref|ZP_06485736.1| specificity determinant for hsdM and hsdR [Xanthomonas campestris
           pv. vasculorum NCPPB702]
          Length = 450

 Score = 53.5 bits (127), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 65/261 (24%), Positives = 111/261 (42%), Gaps = 10/261 (3%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL-PKDGNSRQSDTSTVS 79
           +P  W    I         R  E+ + + YI +  V+ G    + P+     ++ +    
Sbjct: 4   LPAGWVSASIGEICSQGEQRIPEADEQLTYIDIASVDRGRKTVMGPQLLRGYEAPSRARK 63

Query: 80  IFAKGQILYGKLGPYLRK-AIIADF--DGICSTQFLVLQPKDVLPELLQGWLLSIDVTQR 136
           + A G ++     P L   A+I       I ST F VL+P +V P  +   + S    + 
Sbjct: 64  VVATGDVIVSMTRPNLNAVALIGQRHDSAIASTGFDVLRPIEVDPRWIFAAVKSAHFVKA 123

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLK 196
           + A  +GA         I    +P+PPLAEQ  I +K+ A   ++DTL         LLK
Sbjct: 124 MSAKVQGALYPAIKADDIRKHEIPLPPLAEQKRIAQKLDALLAQVDTLKARIDAIPALLK 183

Query: 197 EKKQALVSYIVTKGLNPDVKM---KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIE 253
             ++++V   V   L+ D+++   K    E +G +    EV    A + EL+R  +K   
Sbjct: 184 RFRKSVVHSAVIGRLSADLRVPIEKPEEQEQLGPLELWREVA--LASLGELSRGKSKHRP 241

Query: 254 SNILSLSYGNIIQKLETRNMG 274
            N   L YG+    ++T ++ 
Sbjct: 242 RNDSRL-YGSAYPFIQTGDVA 261



 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 61/117 (52%), Gaps = 3/117 (2%)

Query: 309 QVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSG-LRQSLKFEDVKRLPV 367
           Q  +  I ++ +  ++P  +D  ++   ++S    K   A   G L  ++K +D+++  +
Sbjct: 87  QRHDSAIASTGFDVLRPIEVDPRWIFAAVKSAHFVKAMSAKVQGALYPAIKADDIRKHEI 146

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI--DLR 422
            +PP+ EQ  I   ++   A++D L  +I+    LLK  R S + +AV G++  DLR
Sbjct: 147 PLPPLAEQKRIAQKLDALLAQVDTLKARIDAIPALLKRFRKSVVHSAVIGRLSADLR 203


>gi|167010574|ref|ZP_02275505.1| restriction modification system DNA specificity subunit
           [Francisella tularensis subsp. holarctica FSC200]
          Length = 222

 Score = 53.5 bits (127), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE++E  TG+ +       +   S+   F KG +LYGKL PYL K   ++FD + +T
Sbjct: 100 YVGLENIEGNTGRLIDFCETQGKEIKSSKVEFKKGIVLYGKLRPYLNKVWFSEFDDVATT 159

Query: 110 QFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN--IPMPIPPL 164
           + L   P D   +    ++ + LS    QR+     G+ +       + +    +P+PPL
Sbjct: 160 EILPFYPIDNTRLNMIFVKYYFLSSSYLQRVMRNYSGSRIPRLTTAFLKSEEAYIPLPPL 219

Query: 165 AEQ 167
             Q
Sbjct: 220 PIQ 222


>gi|163754483|ref|ZP_02161605.1| type I restriction-modification system, S subunit [Kordia algicida
           OT-1]
 gi|161325424|gb|EDP96751.1| type I restriction-modification system, S subunit [Kordia algicida
           OT-1]
          Length = 430

 Score = 53.5 bits (127), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 50/208 (24%), Positives = 97/208 (46%), Gaps = 16/208 (7%)

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGN-IIQKLE 269
           +N   K K    E+V  +P+ W++ P  A+  E N K    I   +LS++ G  +I++ E
Sbjct: 1   MNAYPKYKTIAFEYVTQIPEDWDLLPNIAIFEERNEKGH--IHEELLSVTIGKGVIKQSE 58

Query: 270 TRNMGLKPESYETYQIVDPGEIVF--RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPH- 326
                        Y++V+ G+IV+  RF       R   S     +G++++A   +KP  
Sbjct: 59  LNKKDSSNPDKSNYKLVEIGDIVYSMRF-------RQGASGYSNYKGLVSNACTVLKPKM 111

Query: 327 GIDSTYLAWLMR--SYDLCKVFYAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVIN 383
            I+  +  +  R   Y      Y+ G +  ++ L+++D KR+   VPP++ Q  I   + 
Sbjct: 112 KINPKFFHYQYRLPFYQNYAERYSYGIADGQKPLRWQDFKRMYAFVPPLETQNQIVTYLE 171

Query: 384 VETARIDVLVEKIEQSIVLLKERRSSFI 411
            +  +I   V+K  + + L + + +S +
Sbjct: 172 EKEKQIKQFVKKKNRIVDLTENQLNSLV 199



 Score = 43.9 bits (102), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 86/397 (21%), Positives = 156/397 (39%), Gaps = 66/397 (16%)

Query: 6   AYPQYKDSGVQWIGAIPKHWKVVP-IKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL 64
           AYP+YK    +++  IP+ W ++P I  F + N     E G   I+  L  V  G G   
Sbjct: 3   AYPKYKTIAFEYVTQIPEDWDLLPNIAIFEERN-----EKGH--IHEELLSVTIGKGVIK 55

Query: 65  PKDGNSRQS---DTSTVSIFAKGQILYGKLGPYLRKAI--IADFDGICSTQFLVLQPKDV 119
             + N + S   D S   +   G I+Y       R+     +++ G+ S    VL+PK  
Sbjct: 56  QSELNKKDSSNPDKSNYKLVEIGDIVYSMR---FRQGASGYSNYKGLVSNACTVLKPKMK 112

Query: 120 LPELLQGWLLSIDVTQRIEAICEGATMSHAD------WKGIGNIPMPIPPLAEQVLIREK 173
           +      +   +   Q      E  +   AD      W+    +   +PPL  Q  I   
Sbjct: 113 INPKFFHYQYRLPFYQN---YAERYSYGIADGQKPLRWQDFKRMYAFVPPLETQNQIVTY 169

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
           +  +  +I   + ++ R ++L + +  +LV      G N     KD    W  L    W+
Sbjct: 170 LEEKEKQIKQFVKKKNRIVDLTENQLNSLVF-----GKNKYTDFKD----WKDLFNTSWK 220

Query: 234 VKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETY---------Q 284
           ++    + +E N KN               ++   + R +  K E  E Y         +
Sbjct: 221 IEKAKWVFSERNIKNH----------PSERLLASTQDRGLVFKDEIEENYVTATQTDGLK 270

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAY--MAVKPHGID----STYLAWLMR 338
           +V   + V   I L++ +  +  ++V  +GI + AY    +K    D      Y  +L +
Sbjct: 271 LVCKNDFV---ISLRSFEGGIELSEV--QGITSPAYNIFYLKKEFNDIKNLKYYYKYLFK 325

Query: 339 SYDLCKVFYAMGSGLRQ--SLKFEDVKRLPVLVPPIK 373
           S     +   + SG+R+  ++ F+D + L + +P  K
Sbjct: 326 SNQFIGLLNTVVSGIREGKNISFKDFRELYIPIPDKK 362


>gi|260641864|ref|ZP_05413806.2| type I restriction-modification system, S subunit [Bacteroides
           finegoldii DSM 17565]
 gi|260624415|gb|EEX47286.1| type I restriction-modification system, S subunit [Bacteroides
           finegoldii DSM 17565]
          Length = 353

 Score = 53.5 bits (127), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 77/179 (43%), Gaps = 14/179 (7%)

Query: 23  KHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFA 82
           K WK   IK        +   SGK I  + L+ +ES TG+ + K     ++  S  S F 
Sbjct: 16  KGWKTAKIKDVAPEMPSKEQLSGK-IWLLNLDMIESNTGRIIEKVYEDVENALSVQS-FD 73

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP------KDVLPELLQGWLLSIDVTQR 136
           +G +L+ KL PYL K +I D  G+ +T+ + L+P      K  L  LL+G          
Sbjct: 74  EGNVLFSKLRPYLNKVVIPDEPGMATTELVPLRPEPSKLHKVFLSHLLRG----NQFVNY 129

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
              I  G  M       + N    +PP+ +Q+      IAE V        + +FIE+ 
Sbjct: 130 ANDIAGGTKMPRMPLTELRNFDCILPPMDKQLEFV--FIAEQVDKSKFGDFKSQFIEMF 186


>gi|63146884|emb|CAI79467.1| HsdS-type I specificity subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 401

 Score = 53.5 bits (127), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 84/335 (25%), Positives = 130/335 (38%), Gaps = 30/335 (8%)

Query: 54  EDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV 113
           +D+  G G  L K+  S+ +    +  F  G +L+GKL PYL+  + A F+G+    F V
Sbjct: 47  DDINPGMGT-LNKEPKSKGTSKRGIH-FNPGDVLFGKLRPYLKNWLFACFEGVAVGDFWV 104

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP-LAEQVLIRE 172
           L    +        L+     Q I  +  G+ M  +DW  + N    IP  L+EQ  I  
Sbjct: 105 LTSSKIDHGFTYS-LIQAPEFQYIANLSSGSKMPRSDWGLVSNARTFIPTNLSEQKSISS 163

Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHW 232
            +      I TL  E+ R +E LK     L      K   P V+ K     W     D  
Sbjct: 164 VLFGLDTAI-TLHEEKKRQLERLKS--ALLQKMFADKSGYPAVRFKGFDDIW-----DQE 215

Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSYGNII--QKLETRNMGLKPESYETYQIVDPGE 290
           ++     L   L      + +S I  L   NI+  Q + T +      S      V  G+
Sbjct: 216 KLNSLVRLHRGLTYSPNNVQDSGIRILRSSNILDGQFVMTDDDIFVKSSVVNIPTVKDGD 275

Query: 291 IVFRFIDLQNDKRSLRSAQVMERGI-----ITSAYMAVK----PHGIDSTY-LAWLMRSY 340
           I+   I   N    L     +  GI     ++  +M V     P  ++S +  +W  R  
Sbjct: 276 IL---ITAANGSIKLVGKHAIISGISENTAVSGGFMLVGSSRIPDFVNSLFDTSWYQR-- 330

Query: 341 DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQ 375
              + +   G+G   +LK  D+ +  V VP   EQ
Sbjct: 331 -FIRKYVTGGNGSIGNLKKNDLDKQYVKVPTTSEQ 364


>gi|254367478|ref|ZP_04983504.1| type I restriction-modification system, subunit R [Francisella
           tularensis subsp. holarctica 257]
 gi|134253294|gb|EBA52388.1| type I restriction-modification system, subunit R [Francisella
           tularensis subsp. holarctica 257]
          Length = 225

 Score = 53.5 bits (127), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE++E  TG+ +       +   S+   F KG +LYGKL PYL K   ++FD + +T
Sbjct: 103 YVGLENIEGNTGRLIDFCETQGKEIKSSKVEFKKGIVLYGKLRPYLNKVWFSEFDDVATT 162

Query: 110 QFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN--IPMPIPPL 164
           + L   P D   +    ++ + LS    QR+     G+ +       + +    +P+PPL
Sbjct: 163 EILPFYPIDNTRLNMIFVKYYFLSSSYLQRVMRNYSGSRIPRLTTAFLKSEEAYIPLPPL 222

Query: 165 AEQ 167
             Q
Sbjct: 223 PIQ 225


>gi|30250445|ref|NP_842515.1| restriction modification system, type I [Nitrosomonas europaea ATCC
           19718]
 gi|30139286|emb|CAD86438.1| Restriction modification system, type I [Nitrosomonas europaea ATCC
           19718]
          Length = 396

 Score = 53.5 bits (127), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 45/90 (50%), Gaps = 3/90 (3%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ---PKDVLPELLQGWLLSIDVTQRI 137
           F  GQ+LYG    YLRK  +ADF+GIC+    VL+   P ++LPE L   + +       
Sbjct: 68  FKPGQVLYGSRRTYLRKVAVADFEGICANTTFVLEPHNPNELLPEFLPFLMQTEAFNDFS 127

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
               +G+   + ++  +      +PP+ EQ
Sbjct: 128 VKNSKGSVNPYINFSDLAKFEFVLPPIDEQ 157


>gi|160889099|ref|ZP_02070102.1| hypothetical protein BACUNI_01520 [Bacteroides uniformis ATCC 8492]
 gi|156861566|gb|EDO54997.1| hypothetical protein BACUNI_01520 [Bacteroides uniformis ATCC 8492]
          Length = 385

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 77/179 (43%), Gaps = 14/179 (7%)

Query: 23  KHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFA 82
           K WK   IK        +   SGK I  + L+ +ES TG+ + K     ++  S  S F 
Sbjct: 16  KGWKTAKIKDVAPEMPSKEQLSGK-IWLLNLDMIESNTGRIIEKVYEDVENALSVQS-FD 73

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP------KDVLPELLQGWLLSIDVTQR 136
           +G +L+ KL PYL K +I D  G+ +T+ + L+P      K  L  LL+G          
Sbjct: 74  EGNVLFSKLRPYLNKVVIPDEPGMATTELVPLRPEPSKLHKVFLSHLLRGN----QFVNY 129

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
              I  G  M       + N    +PP+ +Q+      IAE V        + +FIE+ 
Sbjct: 130 ANDIAGGTKMPRMPLTELRNFDCILPPMDKQLEF--VFIAEQVDKSKFGDFKSQFIEMF 186


>gi|153808175|ref|ZP_01960843.1| hypothetical protein BACCAC_02461 [Bacteroides caccae ATCC 43185]
 gi|149129078|gb|EDM20294.1| hypothetical protein BACCAC_02461 [Bacteroides caccae ATCC 43185]
          Length = 473

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 85/381 (22%), Positives = 159/381 (41%), Gaps = 50/381 (13%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           LED+E  T   +       ++       F KG +LY KL  YL K ++A   G C+T+ +
Sbjct: 106 LEDLEKDTASIIQMLSKKERNIKGVRHKFDKGDVLYSKLRTYLNKVLVAPKTGYCTTEII 165

Query: 113 VLQPKDVLPELLQGWLLS----IDVTQRIEAICEGATMSHAD-WKGIGNIPMPIPPLAEQ 167
                  +       +L     +D TQ+     +   +S  D  KG+    +P+PP+AEQ
Sbjct: 166 PFNSYCGISNFYLCHVLRSAYFLDYTQQCGYGVKMPRLSTNDACKGM----IPLPPIAEQ 221

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
             I  +I      ID +  +++     +K+ K  ++   +   L P        IE +  
Sbjct: 222 QRIVVEIEKWFALIDQVEQDKVDLQTTIKQTKSKILDLAIHGKLVPQDPNDKPAIELLKR 281

Query: 228 V-PD-------HWEVKPF-------FALVTELNRKNTKLIESNILSLSYGNIIQKLETRN 272
           + PD       H+   PF       +  + E+ +  +    S +    Y   I  L+T +
Sbjct: 282 INPDFTPCDNGHYPNFPFDIPKKWNWVTLGEIGKWQSGSTPSRLNKDYYNGDIPWLKTGD 341

Query: 273 MGLKPESYETYQIVDPGEIVFRFIDLQNDK--------RSLRSAQVMERGIIT------S 318
           +    + Y T+    P  I  + ++  + K         ++  A + + GI+T       
Sbjct: 342 LN---DGYITHI---PEYITEKALNETSVKLNPTGSILMAMYGATIGKLGILTYPATTNQ 395

Query: 319 AYMAVKPH-GIDSTYLAWLMRSY--DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQ 375
           A  A + + GI+  +L + + S+  D  K+    G G + ++  E +    + +PP +EQ
Sbjct: 396 ACCACEIYTGIEKEFLFYFLLSHRADFIKL---GGGGAQPNISKEKIINTYIPLPPSEEQ 452

Query: 376 FDITNVINVETARIDVLVEKI 396
             I N +N   A++DV++E +
Sbjct: 453 KRIVNAVNDVFAQLDVIMESL 473


>gi|290953273|ref|ZP_06557894.1| type I restriction-modification system, subunit S [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295313479|ref|ZP_06804075.1| type I restriction-modification system, subunit S [Francisella
           tularensis subsp. holarctica URFT1]
          Length = 225

 Score = 53.1 bits (126), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE++E  TG+ +       +   S+   F KG +LYGKL PYL K   ++FD + +T
Sbjct: 103 YVGLENIEGNTGRLIDFCETQGKEIKSSKVEFKKGIVLYGKLRPYLNKVWFSEFDDVATT 162

Query: 110 QFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN--IPMPIPPL 164
           + L   P D   +    ++ + LS    QR+     G+ +       + +    +P+PPL
Sbjct: 163 EILPFYPIDNTRLNMIFVKYYFLSSSYLQRVMRNYSGSRIPRLTTAFLKSEEAYIPLPPL 222

Query: 165 AEQ 167
             Q
Sbjct: 223 PIQ 225


>gi|284048512|ref|YP_003398851.1| restriction modification system DNA specificity domain protein
           [Acidaminococcus fermentans DSM 20731]
 gi|283952733|gb|ADB47536.1| restriction modification system DNA specificity domain protein
           [Acidaminococcus fermentans DSM 20731]
          Length = 384

 Score = 53.1 bits (126), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 60/247 (24%), Positives = 106/247 (42%), Gaps = 22/247 (8%)

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVK 216
           + + +P   EQ    EK+      ID+LIT   R  E+LK+ K++ +  +  K      +
Sbjct: 141 LDLLLPEHKEQ----EKLGNYFSHIDSLITLHQRKYEMLKKIKKSFLEKMFPKNGKRVPE 196

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           ++ SG        D WE +   A+  E + K    + +  +    G I +    RN+   
Sbjct: 197 LRFSGF------TDDWEQRKLGAIFEEYSDKGHPNLSALTIIQGGGTIRRDDSDRNLQYD 250

Query: 277 PESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWL 336
            +S   Y+ V+ G+ +   + L++ +  L  A     GII+ AY      G DS +    
Sbjct: 251 KKSLANYKKVETGDFI---VHLRSFEGGLEKATT--SGIISPAYHTFHGEGTDSRFYYCY 305

Query: 337 MRS-----YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
            RS     +DL    Y +  G  +S+  E +K + +    ++EQ  I N I+     I +
Sbjct: 306 FRSERFINHDLKPHVYGIRDG--RSIDIEGMKTINIPWTKVEEQKAIGNYIDCLDNLITL 363

Query: 392 LVEKIEQ 398
              K+E+
Sbjct: 364 HQRKLEK 370


>gi|324115278|gb|EGC09242.1| type I restriction modification DNA specificity domain-containing
           protein [Escherichia fergusonii B253]
          Length = 449

 Score = 53.1 bits (126), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 97/435 (22%), Positives = 172/435 (39%), Gaps = 65/435 (14%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRT------SESGKDIIYIGLEDVESG-----TGKYLPKD 67
           G +P+ W    +     + TG+T      S  G +I +I   D++ G     T   L + 
Sbjct: 4   GKLPEGWVECELSELGNIVTGKTPSTKEPSNFGGNIPFIKPGDLDLGGYIMNTADTLTEK 63

Query: 68  GNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE----- 122
           G S        S+        GK+G  ++K+         + Q   L P + L       
Sbjct: 64  GLSLVPTLPANSVVVTCIGNLGKVGITVKKSA-------SNQQINALIPSEKLNVKFVYY 116

Query: 123 ---LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV 179
               L+ WL S      I AI   +  S A        P   PPLAEQ +I EK+     
Sbjct: 117 QILTLKPWLESQSAATTI-AIVNKSKFSQA--------PFKFPPLAEQKIIAEKLDTLLA 167

Query: 180 RIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL--VPDHWEVKPF 237
           ++++      +  ++LK  +QA+++  V   L           EW  L  +   W     
Sbjct: 168 QVESTKARLEQIPQILKRFRQAVLAIAVNGQLTK---------EWRELSELSAIWPSLTL 218

Query: 238 FALVTELNRKNTKLIESNILSLSYG-NIIQKLETR---------NMGLKPESYETYQIVD 287
             LVT     + + I+  I +   G N I+  + R            + PE  +  + V 
Sbjct: 219 GELVTIERGSSPRPIKDYITASESGVNWIKIGDAREGEKYIHSTKEKITPEGAKKSRKVT 278

Query: 288 PGEIVFRFIDLQNDKRSLRSAQVME-RGIITSAYMAVK-PHGIDSTYLAWLMRSYDLCKV 345
           PG+ +       ++  SL  A +++  G +   +  ++ P  ID  Y  +L+ S  L + 
Sbjct: 279 PGDFIL------SNSMSLGRAYIVDIEGYVHDGWFILRLPQHIDKNYFYYLLSSSQLQEQ 332

Query: 346 FYAMG-SGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
           F  +   G+ Q+++ E VK+  V +P  KEQ +I   +    A  D + +++  ++  + 
Sbjct: 333 FSNLAVGGVVQNIRSELVKQAIVNIPSEKEQHEIVRRVEQLFAYADTIEKQVNNALARVN 392

Query: 405 ERRSSFIAAAVTGQI 419
               S +A A  G++
Sbjct: 393 NLTQSILAKAFRGEL 407


>gi|259508262|ref|ZP_05751162.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
 gi|259164150|gb|EEW48704.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
          Length = 329

 Score = 52.8 bits (125), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/300 (20%), Positives = 129/300 (43%), Gaps = 33/300 (11%)

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLK 196
           ++A   G+T +      + ++P+P+  L +Q  I + +  ET  ID +  E  + ++L+ 
Sbjct: 35  LQAAGRGSTFTEVSASDVASLPIPVTSLDKQDWIADYLDRETAEIDAMAVELDQAMDLID 94

Query: 197 EKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLI---- 252
           E+  A V         P + ++ S I+               ++ T  +    K      
Sbjct: 95  ERFHAEVEQSFQSLDAPRMPLR-SQIQ---------------SMTTGTSVTAAKFAPAAG 138

Query: 253 ESNILSLS--YGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV 310
           E  +L+ S  +G+ + +   +++    + +E  ++  P  I    +   N    +  A  
Sbjct: 139 EPGVLATSAVFGDELNETAVKSV----DPHEYVRLTCPLRINTLLVSRMNTMNLVGKAVT 194

Query: 311 MERGIITSAYMAVKPHGID---STYLAWLMRSYDLCKVFYAMGSGLRQSLKF---EDVKR 364
           + R +    Y+  +   ++     Y+ W  RS    +    +  G   S+K    +  + 
Sbjct: 195 VGRHL-PDVYLPDRLWAVEVDVPRYIYWWTRSQSYREQIRGLAVGASDSMKTLSQQAFRS 253

Query: 365 LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGE 424
           + + VPP+ +Q  +   ++    R   L  +++++  LL+ERR+  I+AAVTGQID+  +
Sbjct: 254 ITLPVPPVTQQIAVAAQLDEAAERFSALKAELQEAKGLLEERRAVLISAAVTGQIDVSAQ 313


>gi|163784191|ref|ZP_02179124.1| type I restriction-modification enzyme, S subunit [Hydrogenivirga
           sp. 128-5-R1-1]
 gi|159880541|gb|EDP74112.1| type I restriction-modification enzyme, S subunit [Hydrogenivirga
           sp. 128-5-R1-1]
          Length = 475

 Score = 52.8 bits (125), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 99/443 (22%), Positives = 189/443 (42%), Gaps = 59/443 (13%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTS-----ESGKDIIYIGLEDVES---------GTGKYLPK 66
           IP+ W+VV +    ++  G+T      +  K    I ++D E+         G   ++  
Sbjct: 2   IPEDWEVVRLGDIAEIQQGKTPKRDLYDDRKGYRIIKVKDFENEKFVKHYPNGERSFVKV 61

Query: 67  DGNSR----QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE 122
           D  +R    Q D   +S     +++  K+G Y    + ++      ++ L ++  +    
Sbjct: 62  DLGNRYTLEQGDILILSAGHSSKVVGQKIGFY---NVNSNNKVFFVSELLRIRANNKTNP 118

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETV-RI 181
           L      SI   +  + I E     H   + + N+ +P+PPL EQ     K IA  + +I
Sbjct: 119 LF--LFFSIISQKSRKQIKEEIKGGHLYPRDLVNLKIPLPPLPEQ-----KAIATVLDKI 171

Query: 182 DTLITERIRFIELLKEKKQALVSYIVTKGLNP-----DVKMKDSGIEWVGLVPDHWEVKP 236
              I +    I+  KE K++L+ +  T G+ P      VK+K++ I   GL+P+HWE+K 
Sbjct: 172 RQAIEQTEEVIQANKELKKSLMKHFFTYGVVPPEETDKVKLKETEI---GLIPEHWEIKT 228

Query: 237 FFALVTELNRKNTKLIESN-----ILSLSYGNIIQK---LETRNMGLKPESYETYQ-IVD 287
               V  +    +  I +N     I  +S  +I ++   L  +   +KP    T + I+ 
Sbjct: 229 LKDSVDSIEYGYSVSIPANEDQKGIPIISTADITKEGKLLYNKIRKIKPPKRLTEKLILK 288

Query: 288 PGEIVFRFIDLQN--DKRSLRSAQVMERG---IITSAYMAVKPHGIDST--YLAWLMRSY 340
            G+++F + +      K ++  A+ + +    I  S  + ++    +S   YL +L+  Y
Sbjct: 289 DGDVLFNWRNSPELIGKTTVFEAEKVSKDDFYIYASFILRIRSKESESNNFYLKYLLNYY 348

Query: 341 DLCKVFYAMGSGLRQSLKF--EDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
                F  +         +   ++  L + +PPI EQ  I  ++N    +ID  +E  E 
Sbjct: 349 REIGTFIKLARRAVNQANYNRNEIYNLKIPLPPIDEQKQIAKILN----KIDNKIEAEEN 404

Query: 399 SIVLLKERRSSFIAAAVTGQIDL 421
               L++   S +   +TG+I L
Sbjct: 405 KKEALEKLFKSLLNNLMTGKIRL 427


>gi|194442247|ref|YP_002043768.1| putative type I restriction-modification system S subunit
           [Salmonella enterica subsp. enterica serovar Newport
           str. SL254]
 gi|194400910|gb|ACF61132.1| putative type I restriction-modification system, S subunit
           [Salmonella enterica subsp. enterica serovar Newport
           str. SL254]
          Length = 571

 Score = 52.8 bits (125), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/135 (26%), Positives = 67/135 (49%), Gaps = 8/135 (5%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           LED+E  T K + K   + +   S+ + F++G +LYGKL PYL K I+A+  G+C+T+ +
Sbjct: 136 LEDIEKVTSKLINKVTFAERPFKSSKNRFSQGDVLYGKLRPYLDKVIVANEPGVCTTEII 195

Query: 113 -VLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
            +    ++ PE L+  L + +      +   G  +     +      + + P+ EQ+ I 
Sbjct: 196 PITSYGNIYPEFLRLLLKAPNFIIYANSSTHGMNLPRLGTEKAQQAVIELAPIQEQLRI- 254

Query: 172 EKIIAETVRIDTLIT 186
                   R+D L++
Sbjct: 255 ------VSRVDKLMS 263


>gi|256825201|ref|YP_003149161.1| hypothetical protein Ksed_13680 [Kytococcus sedentarius DSM 20547]
 gi|256688594|gb|ACV06396.1| hypothetical protein Ksed_13680 [Kytococcus sedentarius DSM 20547]
          Length = 354

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 81/371 (21%), Positives = 159/371 (42%), Gaps = 60/371 (16%)

Query: 80  IFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPE-----LLQGWLLSIDVT 134
           +F K  I  G +G       +A  DG+ +  + V++P+  +       L++      ++ 
Sbjct: 1   MFNKMSIRDGAMG-------LAREDGLVTYHYEVMRPRPAVEARYVVYLMKSSWFGGELI 53

Query: 135 QRIEAI----CEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIR 190
           +R   I     +G   +   ++ +  I   IP +  Q  I + +  ET +ID++I  +  
Sbjct: 54  KRERGIGAGGAKGVRTTEVPFRVLRTIDCYIPTVEGQRAIADFLDRETAQIDSMIEAQNV 113

Query: 191 FIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTK 250
            ++ L+E+++A +S  +           D+ ++ V          P   L+T +++  + 
Sbjct: 114 LMQELRERQRAAISNTIDS---------DASLQRV----------PLRRLITGISQGWSP 154

Query: 251 LIESN-ILSLSYGNIIQKLETRNMGL-KPESYETYQIVDPG------EIVFRFIDLQNDK 302
             E   +   S    + K+   N G+ +PE  +      PG      E+  R  DL   +
Sbjct: 155 QCEDTPVDDPSTQWSVLKVGCVNGGVFRPEQNKML----PGDLEPRPELGLRAGDLLMSR 210

Query: 303 RSLR----SAQVMERGIITSAY------MAVKPHGIDSTYLAWLM---RSYDLCKVFYAM 349
            + R    SA V++R   T         +AV    + S Y+A  +   ++ D  ++    
Sbjct: 211 GNTREWVGSAAVVDRDYPTLMLSDLLYRVAVDRSLVSSEYVALALSTRKARDEIEIAAKG 270

Query: 350 GSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSS 409
            S   Q +   D++   + +  ++ Q D+ N  +  T R D ++   ++ I LL+ERR +
Sbjct: 271 ASHSMQKVSQGDIRSTTIPLRSLQAQADVVNEASAITVRADAMISAAQEVIDLLRERREA 330

Query: 410 FIAAAVTGQID 420
            I AAVTG+ID
Sbjct: 331 LITAAVTGRID 341



 Score = 41.2 bits (95), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 28/121 (23%), Positives = 63/121 (52%), Gaps = 10/121 (8%)

Query: 312 ERGIITSAYMAVKPH-GIDSTYLAWLMRSY----DLCKVFYAMGSGLRQSLK-----FED 361
           E G++T  Y  ++P   +++ Y+ +LM+S     +L K    +G+G  + ++     F  
Sbjct: 17  EDGLVTYHYEVMRPRPAVEARYVVYLMKSSWFGGELIKRERGIGAGGAKGVRTTEVPFRV 76

Query: 362 VKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
           ++ +   +P ++ Q  I + ++ ETA+ID ++E     +  L+ER+ + I+  +     L
Sbjct: 77  LRTIDCYIPTVEGQRAIADFLDRETAQIDSMIEAQNVLMQELRERQRAAISNTIDSDASL 136

Query: 422 R 422
           +
Sbjct: 137 Q 137



 Score = 38.9 bits (89), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 137 IEAICEGAT--MSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIEL 194
           IE   +GA+  M       I +  +P+  L  Q  +  +  A TVR D +I+     I+L
Sbjct: 264 IEIAAKGASHSMQKVSQGDIRSTTIPLRSLQAQADVVNEASAITVRADAMISAAQEVIDL 323

Query: 195 LKEKKQALVSYIVTKGLNPDV 215
           L+E+++AL++  VT  ++P+ 
Sbjct: 324 LRERREALITAAVTGRIDPET 344


>gi|218439052|ref|YP_002377381.1| restriction modification system DNA specificity domain protein
           [Cyanothece sp. PCC 7424]
 gi|218171780|gb|ACK70513.1| restriction modification system DNA specificity domain protein
           [Cyanothece sp. PCC 7424]
          Length = 417

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/145 (27%), Positives = 73/145 (50%), Gaps = 9/145 (6%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSD--TSTVSIFAKGQILYGKLGPYLRKAIIADFDGIC 107
           +IG++ +++ T +   +D  + + D  TS   +F  G ILY K+ PYLRK+++ DF+G+C
Sbjct: 254 HIGVDVIQANTCQL--EDYRTIEEDGVTSGKYLFTSGSILYSKIRPYLRKSVLVDFEGLC 311

Query: 108 STQFLVLQ--PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLA 165
           S     L     ++ P+ L  +L+S   T   ++    A +   +   + +  +  P   
Sbjct: 312 SADIYPLSVISDEIEPKFLMWFLISPLFTDYAKSHSGRARIPKINRDALFSFKLVYPNYE 371

Query: 166 EQVLI---REKIIAETVRIDTLITE 187
           EQ+ I    + I  E  +ID L+ E
Sbjct: 372 EQISIISYLDLIRFEVQKIDKLLKE 396


>gi|154487134|ref|ZP_02028541.1| hypothetical protein BIFADO_00974 [Bifidobacterium adolescentis
           L2-32]
 gi|154084997|gb|EDN84042.1| hypothetical protein BIFADO_00974 [Bifidobacterium adolescentis
           L2-32]
          Length = 405

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 75/333 (22%), Positives = 143/333 (42%), Gaps = 40/333 (12%)

Query: 92  GPYLRKAIIADFDGICSTQFLVLQPKDVLPEL-LQGWLLSIDVTQRIEAICEGATMSHAD 150
           GP  R  +  D +G+ S  + V    D + +L L+ +  +    Q +    EG + + +D
Sbjct: 95  GPINRNKL--DRNGVMSPLYTVFSVDDTIDKLYLEHYFKTSRWHQFM--FLEGNSGARSD 150

Query: 151 WKGIGN-----IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSY 205
              I +     +P+  P L EQ    E I +   R+D+LIT   R  + L   K++++  
Sbjct: 151 RFSISDSIFFEMPIQCPVLEEQ----ELIASFFGRLDSLITLHQRKYDKLCVLKKSMLDK 206

Query: 206 IVTKG--LNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGN 263
           +  KG  L P+++       + G   D WE +    L  E + K+   + +  +    G 
Sbjct: 207 MFPKGGSLYPEIR-------FAGFT-DPWEQRKLGELFEEHSEKDRDDLPALTIIQGGGT 258

Query: 264 IIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAV 323
           + +    RN+     S   Y++VD G+ +   + L++ +  L  A     G+++ AY   
Sbjct: 259 VHRDESNRNLQFDRNSLSNYKVVDTGDFI---VHLRSFEGGLEKATCC--GLVSPAYHIF 313

Query: 324 KPHGIDSTYLAWLMRS-----YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDI 378
           +   +DS +     RS      DL    Y +  G  +S+  E +K + +    + EQ  I
Sbjct: 314 RGKNVDSDFYYLYFRSKRFIDADLKPHVYGIRDG--RSIDIEGMKTIFIPWTNLAEQRRI 371

Query: 379 TNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
               +    R+D L+   ++ + LL+  + S +
Sbjct: 372 GAFFD----RLDSLITLHQRKLELLRNIKKSML 400


>gi|315222640|ref|ZP_07864529.1| type I restriction modification DNA specificity domain protein
           [Streptococcus anginosus F0211]
 gi|315188326|gb|EFU22052.1| type I restriction modification DNA specificity domain protein
           [Streptococcus anginosus F0211]
          Length = 339

 Score = 52.0 bits (123), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 89/189 (47%), Gaps = 23/189 (12%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE ++S +  Y+ + G         + I  KG +L+GK   Y +K  IA FDGI S 
Sbjct: 27  YLGLEHLDSDS-IYITRYGADVAPKGDKL-IMKKGDVLFGKRRAYQKKVAIAPFDGIFSA 84

Query: 110 QFLVLQP------KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
             +VL+P      KD  P  ++     +D   +I     G+     +W+ +  +   +P 
Sbjct: 85  HGMVLRPKEDVIDKDFFPMFIKSDYF-LDAAIKISV---GSLSPTINWRDLKELKFELPS 140

Query: 164 LAEQVLIREKIIA-----ETVRIDTLITERI---RFIELLKEKKQALVSYIVT--KGLNP 213
           L EQ  + E + A     +  +   L T+ +   +FIE+  + K+ ++S + T   G +P
Sbjct: 141 LEEQRKLAEVLWAIYDMKDKYKKLILATDELVKSQFIEMFTDVKKGILSDMATIIMGQSP 200

Query: 214 DVKM-KDSG 221
           D K   D+G
Sbjct: 201 DGKTYNDTG 209


>gi|119510902|ref|ZP_01630025.1| putative type I restriction enzyme specificity protein [Nodularia
           spumigena CCY9414]
 gi|119464430|gb|EAW45344.1| putative type I restriction enzyme specificity protein [Nodularia
           spumigena CCY9414]
          Length = 60

 Score = 52.0 bits (123), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 368 LVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR 422
           ++PP  EQ  IT+ +N E  +I     KI+++I LLKE R+S I  AVTG+ID+R
Sbjct: 1   MIPPFNEQLQITDFLNKEMQKIYQQKAKIKEAIELLKEYRTSLITNAVTGKIDVR 55


>gi|227834295|ref|YP_002836002.1| hypothetical protein cauri_2473 [Corynebacterium aurimucosum ATCC
           700975]
 gi|227455311|gb|ACP34064.1| hypothetical protein cauri_2473 [Corynebacterium aurimucosum ATCC
           700975]
          Length = 378

 Score = 52.0 bits (123), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 39/78 (50%)

Query: 41  TSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII 100
           TSE   D+ +I   ++ SG+  ++          TS    F  G ILY K+ PYL K  I
Sbjct: 211 TSEPYMDMPHIAPNNLSSGSDDFVGVKSAVEDRVTSGKYAFQAGDILYSKIRPYLNKVSI 270

Query: 101 ADFDGICSTQFLVLQPKD 118
           A +DG+CS     L P++
Sbjct: 271 AAYDGVCSADMYALVPRN 288


>gi|262183025|ref|ZP_06042446.1| hypothetical protein CaurA7_03452 [Corynebacterium aurimucosum ATCC
           700975]
          Length = 295

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 39/78 (50%)

Query: 41  TSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAII 100
           TSE   D+ +I   ++ SG+  ++          TS    F  G ILY K+ PYL K  I
Sbjct: 128 TSEPYMDMPHIAPNNLSSGSDDFVGVKSAVEDRVTSGKYAFQAGDILYSKIRPYLNKVSI 187

Query: 101 ADFDGICSTQFLVLQPKD 118
           A +DG+CS     L P++
Sbjct: 188 AAYDGVCSADMYALVPRN 205


>gi|254369156|ref|ZP_04985168.1| predicted protein [Francisella tularensis subsp. holarctica FSC022]
 gi|157122106|gb|EDO66246.1| predicted protein [Francisella tularensis subsp. holarctica FSC022]
          Length = 225

 Score = 51.6 bits (122), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 59/123 (47%), Gaps = 5/123 (4%)

Query: 50  YIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICST 109
           Y+GLE++E  TG+ +       +   S+   F KG +LYGKL  YL K   ++FD + +T
Sbjct: 103 YVGLENIEGNTGRLIDFCETQGKEIKSSKVEFKKGIVLYGKLRLYLNKVWFSEFDDVATT 162

Query: 110 QFLVLQPKD---VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGN--IPMPIPPL 164
           + L   P D   +    ++ + LS    QR+     G+ M       + +    +P+PPL
Sbjct: 163 EILPFYPIDNTRLNMIFVKYYFLSSSYLQRVMRNYSGSRMPRLTTAFLKSEEAYIPLPPL 222

Query: 165 AEQ 167
             Q
Sbjct: 223 PIQ 225


>gi|91213998|ref|YP_543984.1| EcoKI restriction-modification system protein HsdS [Escherichia
           coli UTI89]
 gi|117626660|ref|YP_859983.1| specificity determinant for hsdM and hsdR [Escherichia coli APEC
           O1]
 gi|91075572|gb|ABE10453.1| HsdS, type I site-specific deoxyribonuclease [Escherichia coli
           UTI89]
 gi|115515784|gb|ABJ03859.1| HsdS, type I site-specific deoxyribonuclease [Escherichia coli APEC
           O1]
 gi|294493695|gb|ADE92451.1| type I restriction modification DNA specificity protein
           [Escherichia coli IHE3034]
 gi|307629515|gb|ADN73819.1| EcoKI restriction-modification system protein HsdS [Escherichia
           coli UM146]
 gi|323950568|gb|EGB46446.1| type I restriction modification DNA specificity domain-containing
           protein [Escherichia coli H252]
          Length = 455

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 88/426 (20%), Positives = 174/426 (40%), Gaps = 41/426 (9%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRT---------SESGKDIIYIGLEDVESGTGKYL---PK 66
           G +P+ W+ + I     + +G T         + SG+ + ++   D+     KY+    +
Sbjct: 4   GKLPEGWEQIEIGDIADVISGGTPKSGVAENFAPSGEGVAWLTPADLSGYKEKYISHGAR 63

Query: 67  DGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAI----IADFDGICSTQFLVLQPKDVLPE 122
           D  +    + +  +  KG IL+    P    AI    IA   G  S  F    P D+ P+
Sbjct: 64  DLTTLGYSSCSAKLMPKGTILFSSRAPIGYVAIAANEIATNQGFKSFAF----PSDIFPD 119

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
               +L +I      E +  G T           +P  + P AEQ +I EK+     ++D
Sbjct: 120 YAYYFLRNI--RHIAEEMGTGTTFKEISGSSAKTLPFVLVPFAEQKIIAEKLDTLLAQVD 177

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVT 242
           +      +  ++LK  +QA++   V   L  D +   S   W       +  KP +   +
Sbjct: 178 STKARLEQIPQILKRFRQAVLGAAVRGKLTEDWRDNSSLSGWREGKLGEFIKKPSYGTSS 237

Query: 243 ELNRKNTKLIESNILSLSYGNII-QKLETRNMGLKPESYETYQI-VDPGEIVFRFIDLQN 300
           + N+      E  I  L  GN+   KL+  ++    ++ E  +  ++  +++F   +  N
Sbjct: 238 KSNK------EGLIPVLRMGNLQGGKLDWTDLVYTSDTIEIEKYKLEYNDVLF---NRTN 288

Query: 301 DKRSLRSAQVM--ERGIITSAYM---AVKPHGIDSTYLAWLMRSYDLCKVFYAMGS-GLR 354
               +    +   E+  I + Y+      P  ++  YL + + S    +  Y++ S G+ 
Sbjct: 289 SPELVGKTAIYKSEQPAIYAGYLIRVQCLPD-LNPDYLNYHLNSILGRQYCYSVKSDGVS 347

Query: 355 QS-LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAA 413
           QS +  + +   P+ VPP+ EQ +I   +    A  D + +++  ++  +     S +A 
Sbjct: 348 QSNINAQKLIAYPITVPPLPEQAEIVRRVEQLFAYADTIEKQVNNALARVNNLTQSILAK 407

Query: 414 AVTGQI 419
           A  G++
Sbjct: 408 AFRGEL 413


>gi|308183634|ref|YP_003927761.1| putative type I restriction enzyme (specificity subunit)
           [Helicobacter pylori PeCan4]
 gi|308065819|gb|ADO07711.1| putative type I restriction enzyme (specificity subunit)
           [Helicobacter pylori PeCan4]
          Length = 399

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 98/401 (24%), Positives = 160/401 (39%), Gaps = 50/401 (12%)

Query: 20  AIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVS 79
           A+P +W+ V +    ++N   T  +     YI LE+VE G  + L K   ++    S   
Sbjct: 5   ALPLNWQRVRLGDIAEINPPTTIPNV--FYYIDLENVEKG--QLLNKQLMTKNKAPSRAR 60

Query: 80  -IFAKGQILYGKLGPYLRKAIIADFDG--ICST---QFLVLQPKDVLPELLQGWLLSIDV 133
            + +K  ILY  + PY R       +G  + ST   Q   LQ     P  L   L S   
Sbjct: 61  RLLSKNDILYQLVRPYQRNNYFFTLNGNYVASTGYAQIRTLQN----PSFLYFALHSNYF 116

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR----IDTLI---- 185
              +   CEG +        +    + IPPL EQ+ I   I++   R    +D LI    
Sbjct: 117 VNAVLDRCEGTSYPAISSNELKKCEVIIPPLNEQIAI-ANILSGLDRYLCALDALILKKE 175

Query: 186 -TERIRFIELLKEKKQALVSYIVTKGLNPD---VKMKDSGIEWVGLVPDHWE--VKPFFA 239
             ++    ELL ++K+        KG N     V++ D GI   GLV    +  +     
Sbjct: 176 GVKKALSFELLSQRKR-------LKGFNQAWQRVRLGDIGITISGLVGKTKQDFINGNAK 228

Query: 240 LVTELNRKNTKLIESNILSLSYGNI-IQKLETRNMGLKPESYETYQIVDPGEIVFRFIDL 298
            +T LN  N  +I+++IL     N+ I   E +N   K + +       P E+    + L
Sbjct: 229 YITFLNVLNNVIIDTSILE----NVKIYPNEKQNSFKKYDLFFNTSSETPKEVGMCAVLL 284

Query: 299 QNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSG-LRQSL 357
            +  +   ++      I   A        +D  +L++L+ S    K F  +  G  R +L
Sbjct: 285 DDIDQVFLNSFCFGFRIFDKA--------VDGLFLSYLINSEIGRKAFENLAQGSTRYNL 336

Query: 358 KFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQ 398
                  + + +PP+ EQ  I N+++     I  L  K  Q
Sbjct: 337 SRSGFNNVCLFLPPLNEQIAIANILSALDNEITSLKNKKRQ 377


>gi|164687375|ref|ZP_02211403.1| hypothetical protein CLOBAR_01016 [Clostridium bartlettii DSM
           16795]
 gi|164603799|gb|EDQ97264.1| hypothetical protein CLOBAR_01016 [Clostridium bartlettii DSM
           16795]
          Length = 380

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 55/123 (44%), Gaps = 2/123 (1%)

Query: 47  DIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGI 106
           +I  + L+ VES TGK +  +  +     S+   F    +LY KL PYL K +I    G 
Sbjct: 217 EIWLLNLDMVESNTGKIIAYNYVTASEVGSSTCTFDTTNVLYSKLRPYLNKVVIPKEIGY 276

Query: 107 CSTQFLVLQP-KDVLPELLQGWLLSIDV-TQRIEAICEGATMSHADWKGIGNIPMPIPPL 164
            +++ + LQP K +L      ++L   V    I     GA M         +  +PIPP+
Sbjct: 277 ATSEMMPLQPVKGILDRYYLAYMLRNKVFVDYISEKVSGAKMPRVTMNDFRDFKVPIPPI 336

Query: 165 AEQ 167
             Q
Sbjct: 337 ELQ 339


>gi|325104013|ref|YP_004273667.1| hypothetical protein Pedsa_1278 [Pedobacter saltans DSM 12145]
 gi|324972861|gb|ADY51845.1| hypothetical protein Pedsa_1278 [Pedobacter saltans DSM 12145]
          Length = 397

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/142 (23%), Positives = 65/142 (45%), Gaps = 10/142 (7%)

Query: 58  SGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKL----GPYLRKAIIADFDGICSTQ--- 110
           S T K +P   N+  +D S   I  KGQ  YG +    G  +  A+  ++D    +Q   
Sbjct: 29  SITKKLIPSIANTVGTDMSAYKIVEKGQFAYGTITSRNGDKISIALADEYDKALVSQIYI 88

Query: 111 -FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ-- 167
            F V+    +LPE L  W    +  +       G+T    DW+ +  + +PIP + +Q  
Sbjct: 89  VFEVIDTNLLLPEYLMMWFSRPEFDRYARYHSHGSTREAFDWEDLCEVELPIPSIEKQRE 148

Query: 168 VLIREKIIAETVRIDTLITERI 189
           ++ + + +   ++++  I E++
Sbjct: 149 IVAQYQAVENKIKVNEQICEQL 170



 Score = 39.7 bits (91), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 34/138 (24%), Positives = 65/138 (47%), Gaps = 15/138 (10%)

Query: 76  STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQ 135
           + V++F KG IL   + PYL+K   A+  G CS   L ++ K+++ +     +L  D  Q
Sbjct: 265 NNVTVFEKGDILISNIRPYLKKIWFANKKGGCSNDVLCIRSKEIVYQFFALNILFND--Q 322

Query: 136 RIEAICEGA---TMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFI 192
             + + +GA    M   D   I         L  ++L+ +K I  T   D  +  R++  
Sbjct: 323 FFDYVMQGAKGTKMPRGDKDWI---------LEYKILLPKKEILATFSKDIELVSRVKIS 373

Query: 193 ELLKEKK-QALVSYIVTK 209
           + ++ +K   L S+++ +
Sbjct: 374 KTIQNQKLTQLQSFLLNR 391


>gi|298384313|ref|ZP_06993873.1| type I restriction-modification enzyme [Bacteroides sp. 1_1_14]
 gi|298262592|gb|EFI05456.1| type I restriction-modification enzyme [Bacteroides sp. 1_1_14]
          Length = 411

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 84/211 (39%), Gaps = 28/211 (13%)

Query: 53  LEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFL 112
           LED+E  T   + K     ++       F KG +LY KL  YL K ++A   G C+T+ +
Sbjct: 65  LEDLEKDTASIIQKLSKKERNIKGVRHKFKKGDVLYSKLRTYLNKVLVAPKAGYCTTEII 124

Query: 113 VLQPK-DVLPELLQGWLLS---IDVTQRIEAICEGATMSHAD-WKGIGNIPMPIPPLAEQ 167
                 D+    L   L S   +D TQ+     +   +S  D  KG+    +P+PPL+EQ
Sbjct: 125 PFNSYCDISTHYLCHVLRSAYFLDYTQQCGYGVKMPRLSTNDACKGM----VPLPPLSEQ 180

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT-----------------KG 210
             I  +I      ID +   +      +K+ K  ++   +                  K 
Sbjct: 181 QRIVMEIDKWLALIDQIEQGKADLQNTIKQTKSKILDLAIHGKLVPQDPNDEPAIKLLKR 240

Query: 211 LNPDVKMKDSGIEWVGLVPDHWEVKPFFALV 241
           +NPD    D+G      +PD W   P   L 
Sbjct: 241 INPDFTPCDNG--HYAQLPDSWSAVPMQMLC 269


>gi|229165872|ref|ZP_04293638.1| hypothetical protein bcere0007_8480 [Bacillus cereus AH621]
 gi|228617577|gb|EEK74636.1| hypothetical protein bcere0007_8480 [Bacillus cereus AH621]
          Length = 413

 Score = 50.8 bits (120), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 67/263 (25%), Positives = 117/263 (44%), Gaps = 31/263 (11%)

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTK-GLN-PDVKMK 218
           +P   EQ  I E   +    ID LI    R +ELLKE K++L+  +  K G N P+++ +
Sbjct: 165 VPNDEEQKKIGEFFAS----IDNLIPLHQRKLELLKETKKSLLQKMFPKNGANIPEIRFE 220

Query: 219 DSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLS--YGNIIQKLETRNMGLK 276
                      D WE +       ++  KN   I S  L+ S  YG II +L+  +  + 
Sbjct: 221 G--------FTDAWEQRKLGEFSEKVTEKNKNNIYSETLTNSAKYG-IINQLDFFDKDIS 271

Query: 277 PE-SYETYQIVDPGEIVF--RFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYL 333
            E + + Y +V P + V+  R  +L      +   ++   G+++  Y   + H +D TYL
Sbjct: 272 NEKNLDGYYVVRPDDFVYNPRISNLA-PVGPINRNKLGRSGVMSPLYYVFRTHNVDKTYL 330

Query: 334 AWLMRSYDLCKVFYAMG--SGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETAR 388
                S +   +F  +   SG R    ++K    + +P+ +P I EQ  I N       +
Sbjct: 331 EKYFSS-NSWHIFMKLNGDSGARSDRFAIKDSVFREMPIPIPSINEQTQIGNFF----KQ 385

Query: 389 IDVLVEKIEQSIVLLKERRSSFI 411
           +D L+   ++ +  LK  + S +
Sbjct: 386 LDNLITLHQRELNSLKNLKKSLL 408


>gi|327490260|gb|EGF22048.1| type I restriction/modification specificity protein [Streptococcus
           sanguinis SK1058]
          Length = 392

 Score = 50.8 bits (120), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 1/97 (1%)

Query: 77  TVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSID-VTQ 135
           T+S+F KG IL   + PY +K  +AD  G CS   LV++  + +      ++LS D    
Sbjct: 62  TISVFQKGDILISNIRPYFKKIWLADKSGGCSNDVLVVRANEKISNRFLYYVLSSDNFFD 121

Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
                 +G  M   D K I    +PI  L EQ  I E
Sbjct: 122 YAVGTSKGTKMPRGDKKAIMKYKVPIYSLVEQEKIAE 158


>gi|149920795|ref|ZP_01909258.1| Restriction modification system, type I [Plesiocystis pacifica
           SIR-1]
 gi|149818313|gb|EDM77765.1| Restriction modification system, type I [Plesiocystis pacifica
           SIR-1]
          Length = 403

 Score = 50.4 bits (119), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 45/90 (50%), Gaps = 3/90 (3%)

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VLPELLQGWLLSIDVTQRI 137
           F  GQ+LYG    YLRK  +A FDG+C+    V++ K    +LPELL   + +    +  
Sbjct: 66  FRPGQVLYGSRRTYLRKVAVAGFDGVCANTTFVVESKSPGILLPELLPFIMTTEAFHEHS 125

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
               +G+   + ++  +      +PPL EQ
Sbjct: 126 VRESKGSVNPYVNFSDLAWYEFALPPLEEQ 155


>gi|312872265|ref|ZP_07732335.1| conserved domain protein [Lactobacillus iners LEAF 2062A-h1]
 gi|311092088|gb|EFQ50462.1| conserved domain protein [Lactobacillus iners LEAF 2062A-h1]
          Length = 378

 Score = 50.4 bits (119), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 61/294 (20%), Positives = 123/294 (41%), Gaps = 38/294 (12%)

Query: 106 ICSTQFLVLQPKDVLPE-LLQGWLLSI----DVTQRIEAICEGATMSHADWKGIGNIPMP 160
           IC+  ++V + K +    LL+ WL       +  + +     G++    +W  + +I + 
Sbjct: 86  ICTEDYVVFRLKKICENILLKEWLYMYFNRSEFDRFVITNSWGSSTEFYNWSDVCDIELH 145

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           +PPLA    I++K +      + ++  +  +   L++ K    +YI       D++ K  
Sbjct: 146 LPPLA----IQQKYVNV---YNAMVANQKAYERGLEDLKLTCDAYI------EDLRRK-- 190

Query: 221 GIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY 280
                      +E++   + +  ++ +N     +N+  L+   + +        L   S 
Sbjct: 191 -----------YELQEIGSYIERIDERNKDNQLTNVKGLT---VYKHFIDTKANLTNVSI 236

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG--IDSTYL-AWLM 337
             Y+IV  G+I +     +N  R L      E  +I+S Y  ++P    + S YL  W  
Sbjct: 237 TNYKIVRVGDIGYVPTTNRNGDR-LACGLCNEDCLISSIYEVIRPDNSKLRSDYLFLWFR 295

Query: 338 RSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDV 391
           RS     V Y      R++  F D++   + +PP++ Q  I ++  V T R D+
Sbjct: 296 RSEFDRYVRYCSWGSARETFDFRDMEEFSIPIPPLEIQNSIADIYKVYTERKDI 349


>gi|302871463|ref|YP_003840099.1| restriction modification system DNA specificity domain
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574322|gb|ADL42113.1| restriction modification system DNA specificity domain
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 457

 Score = 50.4 bits (119), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 99/240 (41%), Gaps = 39/240 (16%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST--- 77
            PK W +V ++R   L +G   + G        E + S  G+++  DG    SD +    
Sbjct: 23  FPKEWTIVSLERDCVLISGLRPKGGA-----SDEGIPSLGGEHITLDGRINFSDVNAKYI 77

Query: 78  ----VSIFAKGQ-----ILYGKLGPY------LRKAIIADFDGICSTQFLVLQPKDVLPE 122
                 I  KG+     IL  K G        L+K    D   I    F++   K  + +
Sbjct: 78  PEKFFKIMTKGKAEENDILINKDGANTGKVAILKKKFYKDI-AINEHLFILRSKKLFVQQ 136

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
            L  WL S    ++I     G+         I N  +P PPL+EQ  I E  I ET  ID
Sbjct: 137 YLFYWLFSRFGQKQITDRITGSAQPGLSSTFIKNFLVPRPPLSEQRKIAE--ILET--ID 192

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGLNPD--------VKMKDSGIEWVGLVPDHWEV 234
             I +    IE  K  KQ L+  ++TKG++ +         K KDS    +G +P+ W+V
Sbjct: 193 NAIEKTDAIIEKYKRIKQGLMQDLLTKGIDENWQIRNEKTHKFKDS---LLGRIPEEWKV 249


>gi|58038319|ref|YP_190288.1| Type I restriction-modification enzyme S subunit [Gluconobacter
           oxydans 621H]
 gi|58000733|gb|AAW59632.1| Type I restriction-modification enzyme S subunit [Gluconobacter
           oxydans 621H]
          Length = 402

 Score = 50.4 bits (119), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 87/418 (20%), Positives = 167/418 (39%), Gaps = 77/418 (18%)

Query: 46  KDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAK-----------GQILYGKLGPY 94
           K+I  IG++ ++   GK  PKD N  Q+  S + + AK           GQ +  +    
Sbjct: 11  KNINEIGIQVIDGDRGKNYPKD-NEFQATGSCLFLSAKNVTKAGFDFSLGQFITSEKHKI 69

Query: 95  LRKAIIADFDGICSTQ-----FLVLQPKD-------------------VLPELLQGWLLS 130
           L K  +   D + +T+     F     K                    + P+ L     S
Sbjct: 70  LNKGAVELGDIVITTRGSIGHFAYYNQKKYQTIRINSGMAILRSNVNYINPDFLYEVCRS 129

Query: 131 IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIR 190
             +  +IE    G+         I    +P+PPL+EQ    +KI A     D  I    +
Sbjct: 130 QIIKTQIEKASFGSAQPQLTIAIIKKFRIPLPPLSEQ----KKIAAILSTWDRAIEGTEK 185

Query: 191 FIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTK 250
            +   +++K+AL+  ++T            G + +      W  K    +   ++ KN  
Sbjct: 186 LLANSQQQKKALMQQLLT------------GKKRLPGFSGKWLWKRSKEIFKSISIKNNP 233

Query: 251 LIESNILSLS--YGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSA 308
           + +  +LS++   G +++ L  R + +   S + Y++V+PG  +           SLRS 
Sbjct: 234 M-DCELLSVTQDQGVVLRSLLERRVVMPDGSVQGYKLVNPGNFII----------SLRSF 282

Query: 309 Q-----VMERGIITSAYMAVKPH-GIDSTYLAWLMRSYDLCKVFYAMGSGLR--QSLKFE 360
           Q        RG+++ AY  +     I++ +  +  +SY+          G+R  + + ++
Sbjct: 283 QGGLEYSYYRGLVSPAYTVLDNKIEIENDFYKFYFKSYNFIGHLAVATIGIRDGKQISYQ 342

Query: 361 DVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           D   + +  PP+ EQ  I  V+       D  +  IE  +V L++ + + +   +TG+
Sbjct: 343 DFSFIKLPYPPLPEQQAIAAVLTTA----DEEITAIESDLVRLRQEKKALMQQLLTGK 396


>gi|315222637|ref|ZP_07864526.1| type I restriction modification DNA specificity domain protein
           [Streptococcus anginosus F0211]
 gi|315188323|gb|EFU22049.1| type I restriction modification DNA specificity domain protein
           [Streptococcus anginosus F0211]
          Length = 357

 Score = 50.1 bits (118), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/112 (27%), Positives = 53/112 (47%), Gaps = 12/112 (10%)

Query: 70  SRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP------KDVLPEL 123
           S  ++ S    F+KG +L+G+   YL+KA +A FDGICS    V++        D+LP +
Sbjct: 45  SDDTENSFTKEFSKGDVLFGRRRAYLKKAAVAPFDGICSGDITVIRAIEDKVDPDLLPFI 104

Query: 124 LQG-WLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
           +Q  +L    V +       G+      W  +    + +P + EQ  + E +
Sbjct: 105 IQNDFLFDFAVGK-----SAGSLSPRVKWTHLKEFAIELPSMPEQSKLAETL 151


>gi|154488694|ref|ZP_02029543.1| hypothetical protein BIFADO_02001 [Bifidobacterium adolescentis
           L2-32]
 gi|154082831|gb|EDN81876.1| hypothetical protein BIFADO_02001 [Bifidobacterium adolescentis
           L2-32]
          Length = 392

 Score = 50.1 bits (118), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 37/151 (24%), Positives = 67/151 (44%), Gaps = 12/151 (7%)

Query: 25  WKVVPIKRFTKLNTGRTSESGK--DIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFA 82
           W + P + F  ++T   ++     D+ +IG++ +ESGTG+       +     S    F 
Sbjct: 206 WPIKPFETFAIIDTHMANDLTPYLDMPHIGIDSIESGTGRLSGYRTVAEDGIISGKYPFT 265

Query: 83  KGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP------KDVLPELLQGWLLSIDVTQR 136
              ++Y K+ P L K  + DF G+CS+    + P      +  L E+++    S    + 
Sbjct: 266 PEHLIYSKIRPSLNKVALPDFSGVCSSDAYPILPIAGECNRVYLAEVMR----SAYFLEY 321

Query: 137 IEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
           I  +   A M   + K +    MP+PP+  Q
Sbjct: 322 ILPLSGRAQMPKVNKKALSGFSMPLPPIELQ 352


>gi|312136019|ref|YP_004003357.1| restriction modification system DNA specificity domain-containing
           protein [Caldicellulosiruptor owensensis OL]
 gi|311776070|gb|ADQ05557.1| restriction modification system DNA specificity domain protein
           [Caldicellulosiruptor owensensis OL]
          Length = 409

 Score = 50.1 bits (118), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 48/164 (29%), Positives = 77/164 (46%), Gaps = 16/164 (9%)

Query: 10  YKDSGVQWI----GAIPKHWKVVPIKRFTKLNTGRTSESGKDI---IYIGLEDVESGTGK 62
           YK SG +++    G IPK WKVV ++     N   + + GK+I    Y+ ++ VE  +  
Sbjct: 203 YKSSGGEFVDSELGPIPKGWKVVKLREILD-NICDSVKPGKEIEGLPYVPIDIVERKSIA 261

Query: 63  YLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK---DV 119
              K   S +   S++  F K  IL G +  Y  K  IA  +G+      VL+PK   D+
Sbjct: 262 L--KQFKSWEEAKSSLIKFKKDDILLGAMRVYFHKVSIAPCEGVTRKTCFVLRPKKRFDL 319

Query: 120 LPELLQGWLLSIDVTQRIEAICEGATMSHADW-KGIGNIPMPIP 162
              LL   +   D  +  +A  +G TM +A W  G+  + + +P
Sbjct: 320 SYTLL--LIFQDDTIKFADAHSKGTTMPYAVWDNGLAEMKIALP 361


>gi|322804999|emb|CBZ02559.1| type I restriction-modification system,specificity subunit S
           [Clostridium botulinum H04402 065]
          Length = 385

 Score = 50.1 bits (118), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 38/149 (25%), Positives = 62/149 (41%), Gaps = 4/149 (2%)

Query: 23  KHWKVVPIKRFTKLNTGRTSE--SGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSI 80
           K+W V     F  ++T  T +    KD  +IG+E +E  TG+ L           S   I
Sbjct: 195 KNWDVSEFNEFATIDTNMTKDFRKYKDYPHIGIECIEKNTGRILEYKLVKNSDLKSGKYI 254

Query: 81  FAKGQILYGKLGPYLRKAIIADFDGICST-QFLVLQPKDVLPELLQGWLLSID-VTQRIE 138
           F    I+Y K+ P L K  +  F G+CS   + +L  + +      G++L  +     I 
Sbjct: 255 FDNRHIIYSKIRPNLNKVALPSFAGVCSADSYPLLCNEKITTRSYLGYVLRSEFFLSYIL 314

Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQ 167
           A      +   + + +    MP PP+  Q
Sbjct: 315 AFSGRTNIPKVNKEQLRGFKMPTPPINLQ 343


>gi|146297668|ref|YP_001181439.1| restriction modification system DNA specificity subunit
           [Caldicellulosiruptor saccharolyticus DSM 8903]
 gi|145411244|gb|ABP68248.1| restriction modification system DNA specificity domain
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 455

 Score = 49.7 bits (117), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 68/255 (26%), Positives = 104/255 (40%), Gaps = 40/255 (15%)

Query: 21  IPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTST--- 77
            PK W +V ++R   L +G   + G        E + S  G+++  DG    SD +    
Sbjct: 23  FPKEWTIVSLERDCVLISGLRPKGGASD-----EGIPSLGGEHITLDGRINFSDVNAKYI 77

Query: 78  ----VSIFAKGQ-----ILYGKLGP------YLRKAIIADFDGICSTQFLVLQPKDVLPE 122
                 I  KG+     IL  K G        L+K    D   I    F++   K  + +
Sbjct: 78  PEKFFKIMTKGKTEENDILINKDGANTGKVAMLKKKFYKDI-AINEHLFIIRSKKLFVQQ 136

Query: 123 LLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRID 182
            L  WL S    ++I     G+         I N  +P PPL EQ  I E  I ET  ID
Sbjct: 137 YLFYWLFSRFGQKQITDRITGSAQPGLSSTFIKNFLVPRPPLPEQRKIAE--ILET--ID 192

Query: 183 TLITERIRFIELLKEKKQALVSYIVTKGL-------NPDVKMKDSGIEW-----VGLVPD 230
           + I +    IE  K  KQ L+  ++TKG+       +   +++D  I+      +G +P+
Sbjct: 193 SAIEKTDAIIEKYKRIKQGLMQDLLTKGVVSEGEGESERWRLRDENIDKFKDSPLGRIPE 252

Query: 231 HWEVKPFFALVTELN 245
            WEV   +  V  +N
Sbjct: 253 EWEVVDVYGRVNLIN 267


>gi|320352394|ref|YP_004193733.1| hypothetical protein Despr_0256 [Desulfobulbus propionicus DSM
          2032]
 gi|320120896|gb|ADW16442.1| hypothetical protein Despr_0256 [Desulfobulbus propionicus DSM
          2032]
          Length = 113

 Score = 49.7 bits (117), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/26 (69%), Positives = 24/26 (92%)

Query: 6  AYPQYKDSGVQWIGAIPKHWKVVPIK 31
          AYP+YKDSGVQW+G +P+HW++ PIK
Sbjct: 5  AYPRYKDSGVQWLGEVPEHWEIRPIK 30



 Score = 41.6 bits (96), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 14/27 (51%), Positives = 23/27 (85%)

Query: 216 KMKDSGIEWVGLVPDHWEVKPFFALVT 242
           + KDSG++W+G VP+HWE++P  A+V+
Sbjct: 8   RYKDSGVQWLGEVPEHWEIRPIKAIVS 34


>gi|21228841|ref|NP_634763.1| type I restriction-modification system specificity subunit
           [Methanosarcina mazei Go1]
 gi|20907364|gb|AAM32435.1| type I restriction-modification system specificity subunit
           [Methanosarcina mazei Go1]
          Length = 406

 Score = 49.7 bits (117), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 74/351 (21%), Positives = 144/351 (41%), Gaps = 44/351 (12%)

Query: 83  KGQILYGKLGPYLRKAIIADFDG--ICSTQFLVLQPKD---VLPELLQGWLLSIDVTQRI 137
           KG I+YG+ G   R+A+I       +C T  + +  K+   + P  L  +L   ++   I
Sbjct: 74  KGDIVYGRRGDIGRRALIKGEQAGWLCGTGCIKISLKNASILEPSFLYYYLGQPEIVSWI 133

Query: 138 EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKE 197
                GATM + +   I +IP+  P L  Q    +KI       D LI    R IE+L++
Sbjct: 134 YNQAIGATMPNLNTSIIRSIPITYPSLTTQ----KKIAYILSSYDDLIENNTRRIEILEQ 189

Query: 198 KKQALVSYIVTKGLNP---DVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIES 254
             + +      K   P   +VKM  S +   G +P  W+V+    ++    +   K  + 
Sbjct: 190 MAKLVYEEWFVKFRFPGHENVKMVPSDL---GEIPKRWKVREVSEILKRF-KAGKKYTQD 245

Query: 255 NILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERG 314
           N+L      +I + E   +G                      D+ +   SL++  ++   
Sbjct: 246 NVLEEGLIPVIDQSEKEILGFHN-------------------DIADHSASLKNPIMIFGD 286

Query: 315 IITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFE----DVKRLPVLVP 370
                 + ++P  +    + +    Y    VF+ +   L Q+ +++    +++   V++P
Sbjct: 287 HTCKIKILIEPFSVGPNVIPFRSEDYPEIFVFFLI-KNLVQTKEYKRHWNELQAKRVVLP 345

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
            +    D  NV+N    +I +L  K +     L++ R   +   ++G+ID+
Sbjct: 346 DVPLAMDFVNVVNPLFKQITLLEHKNQN----LRKTRDLLLPKLISGEIDV 392


>gi|227547713|ref|ZP_03977762.1| EcoA family type I restriction-modification enzyme, S subunit
           [Corynebacterium lipophiloflavum DSM 44291]
 gi|227080211|gb|EEI18174.1| EcoA family type I restriction-modification enzyme, S subunit
           [Corynebacterium lipophiloflavum DSM 44291]
          Length = 264

 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 65/288 (22%), Positives = 119/288 (41%), Gaps = 62/288 (21%)

Query: 157 IPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVK 216
           IP+P+PPL  Q  I + +  E   +D LI E  R +  L  +K  L+  I+ K  +P++ 
Sbjct: 10  IPIPLPPLETQRRIADYLDKEISEMDALIEEFERLVNDLSNRKLMLIDNIIYKS-DPELC 68

Query: 217 MKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLK 276
           +   G+     + D     P F             IE  +  LS   I            
Sbjct: 69  LAPLGLFLAEPITDGPHETPEF-------------IEEGVPFLSVDGIQN---------- 105

Query: 277 PESYETYQIVDPGEIVF---RFIDLQNDKRSLRSAQ------VMERGIIT---------- 317
                       GE+ F   RFI  ++ +R  + A+      +M +   T          
Sbjct: 106 ------------GELTFAGCRFISQEDHERFAKKAKPRTGDILMGKAASTGKIALVKTKR 153

Query: 318 -----SAYMAVKPHG-IDSTYLAWLMRS-YDLCKVFYAMGSGLRQSLKFEDVKRLPVLVP 370
                S    ++P+  ID  +L  +++S +   ++        ++++   D+ R+ + V 
Sbjct: 154 EFNIWSPLAIIRPNASIDPRWLTLVLKSPFSQRQINDLSTFNTQRNIAMGDIPRIRIPVM 213

Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
            I +Q  I + ++ ETA++D L+E+  + I  LK R+++ I   VTG+
Sbjct: 214 EIGKQGQIADELDRETAKMDALIEESTRLIENLKARKNALITEVVTGR 261



 Score = 40.0 bits (92), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 3/59 (5%)

Query: 153 GIGNIP---MPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
            +G+IP   +P+  + +Q  I +++  ET ++D LI E  R IE LK +K AL++ +VT
Sbjct: 201 AMGDIPRIRIPVMEIGKQGQIADELDRETAKMDALIEESTRLIENLKARKNALITEVVT 259


>gi|71900231|ref|ZP_00682369.1| hypothetical protein XfasoDRAFT_2382 [Xylella fastidiosa Ann-1]
 gi|71730004|gb|EAO32097.1| hypothetical protein XfasoDRAFT_2382 [Xylella fastidiosa Ann-1]
          Length = 159

 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 31/112 (27%), Positives = 54/112 (48%), Gaps = 3/112 (2%)

Query: 314 GIITSAYMAVKPHG--IDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPP 371
            +I  A + ++P    +   +L + +RS +   +     +  + +L    VK LP+  P 
Sbjct: 15  AVINQAILGLEPKSNVLVPEFLFFWLRSLER-HIKNLASTSTQANLNAAKVKALPIFFPS 73

Query: 372 IKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG 423
           ++EQ  I   I  E    D  + + E+ I L++E R   I   VTGQ+D+RG
Sbjct: 74  VEEQKQICGWIKNECRIFDDAITRTEEEITLIREYRDRLITDVVTGQVDVRG 125


>gi|237756251|ref|ZP_04584811.1| type I restriction enzyme MjaXIP specificity protein
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237691588|gb|EEP60636.1| type I restriction enzyme MjaXIP specificity protein
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 421

 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 100/228 (43%), Gaps = 27/228 (11%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRT------SESGKDIIYIGLEDVESGTGKYLPKDGNSR 71
           IG IP+ W+V+ +    ++  G++      +  GK I ++       G  ++        
Sbjct: 17  IGLIPEDWEVMRLGEVAEITMGQSPPGDTYNTYGKGIPFL------QGKAEFGNISPKHI 70

Query: 72  QSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSI 131
           +  T  + I  KG +L     P +    IA+ D         L  K+ + E L   LL  
Sbjct: 71  KYTTKPLKIAKKGSVLISVRAP-VGDVNIANMDYCIGRGLASLNLKNGINEFLFYSLLFF 129

Query: 132 DVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRF 191
                IE    G+     + + +  + +P+PPL EQ  I +  I  TV+  T  TE++  
Sbjct: 130 K--HLIEKESYGSVFKAINKENLARLKIPLPPLEEQKAITD--ILSTVQNTTEKTEKV-- 183

Query: 192 IELLKEKKQALVSYIVTKGLNP-----DVKMKDSGIEWVGLVPDHWEV 234
           I   K+ K++++ ++ T G         VK+K+S I   GL+P+ WEV
Sbjct: 184 INATKQLKKSMMKHLFTYGAVAVDEIDKVKLKESEI---GLIPEDWEV 228



 Score = 42.7 bits (99), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 95/222 (42%), Gaps = 40/222 (18%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRT-SESGKD------IIYIGLEDVESGTGKYLPKDGNS 70
           IG IP+ W+VV +        GRT     KD        ++ + D+++      P   N+
Sbjct: 219 IGLIPEDWEVVRLGDIVNFKIGRTPPRKNKDYWTNGKYYWVSISDMKN------PYINNT 272

Query: 71  RQSDTSTVSIFAKGQILYGKLGP----------YLRKAIIADFDGICSTQFLVLQPKD-- 118
            +     VS  A  +I   KL P           + +  I + D   +   + + PK+  
Sbjct: 273 SE----MVSEKAHKEIFKEKLTPAGTLLMSFKLTIGRTAILNVDAYHNEAIISIYPKENK 328

Query: 119 VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAET 178
           VL E L  +L ++D +   +   +G T++ +    +  IP+P+PPL EQ  I        
Sbjct: 329 VLKEFLFYYLPAVDYSNLQDKAIKGNTLNTSK---LNKIPIPLPPLDEQQKI-------- 377

Query: 179 VRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
             I T I ++I+  E  KE  Q L   ++ + +   +++K +
Sbjct: 378 ANILTTIDQKIQAEEKKKEALQNLFKTLLQQLMTGKIRVKKA 419


>gi|120436928|ref|YP_862614.1| type I restriction-modification system DNA specificity subunit
           [Gramella forsetii KT0803]
 gi|117579078|emb|CAL67547.1| type I restriction-modification system DNA specificity subunit
           [Gramella forsetii KT0803]
          Length = 428

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 71/317 (22%), Positives = 136/317 (42%), Gaps = 48/317 (15%)

Query: 127 WLLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLI 185
           WLL  D  QR I +   GAT+ H   K I +  + +P   E + +++KI +     D LI
Sbjct: 122 WLLRTDYYQRYIASSSSGATVKHTSPKKIYSAKLLVP---ESLFVQQKIASILSGYDDLI 178

Query: 186 TERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL-----VPDHWEVKPFFAL 240
              ++ I+LL+EK Q              V+MK  G E V +     +P+ W +      
Sbjct: 179 ENNLKRIKLLEEKAQLTYEEWF-------VRMKFPGHESVVINKETGLPEGWRITK---- 227

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYET---YQIVDP--------- 288
           + +L+  N+K IE      +Y   I+ ++ +  G+ P S ++   Y IVD          
Sbjct: 228 LNKLSGVNSKNIEK-----TYEGDIKYIDIK--GVSPNSIDSLTEYSIVDAPGRAKRIVK 280

Query: 289 -GEIVFRFIDLQNDKRSLRSAQVMERG-IITSAYMAVKPHGIDSTYLAWLMRSYDLCKVF 346
            G+I++  +  + ++RS       E   I ++ +  + P  + ++YL + + +       
Sbjct: 281 HGDIIWSCV--RPNRRSHAVVWKPESNWIASTGFCVISPKKLPTSYLYYFLTTNSFVGYL 338

Query: 347 YAMGSGLRQ-SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
             +  G    ++K +  K   ++VP    + +I    + +  +   L+   +Q    LKE
Sbjct: 339 TNLAGGAAYPAVKADHFKTAEIVVP----KDEIVKAFDEKFEKSLELIWNFKQQNQFLKE 394

Query: 406 RRSSFIAAAVTGQIDLR 422
            R   +   + G I++ 
Sbjct: 395 ARDILLPRLMAGMINVE 411


>gi|135210|sp|P07990|T1S_SALPO RecName: Full=Type-1 restriction enzyme StySPI specificity protein;
           Short=S.StySPI; AltName: Full=Type I restriction enzyme
           StySPI specificity protein; Short=S protein
 gi|79033|pir||A26652 type I site-specific deoxyribonuclease (EC 3.1.21.3) - Salmonella
           sp
 gi|154135|gb|AAA27145.1| hsdS specificity protein [Salmonella enterica subsp. enterica
           serovar Potsdam]
          Length = 463

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 86/428 (20%), Positives = 167/428 (39%), Gaps = 37/428 (8%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIY--------IGLEDVESG---------TG 61
           G +P+ W   P+   T L  G T +  + + Y        I   ++++G           
Sbjct: 4   GKLPEGWATAPVSTVTTLIRGVTYKKEQALNYLQDDYLPIIRANNIQNGKFDTTDLVFVP 63

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVL 120
           K L K+      +   +++ +  + + GK   + R      F   C      L+P K + 
Sbjct: 64  KNLVKESQKISPEDIVIAMSSGSKSVVGK-SAHQRLPFECSFGAFCG----ALRPEKFIS 118

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
           P  +  +  S     +I ++  GA +++        I +PIP LAEQ +I EK+     +
Sbjct: 119 PNYIAHFTKSSFYRNKISSLSAGANINNIKPASFDLINIPIPSLAEQKIIAEKLDTLLAQ 178

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           +D+      +  ++LK  +QA+++  V+  L   ++   S I W         V     L
Sbjct: 179 VDSTKARLEQIPQILKRFRQAVLAAAVSGTLTTALRNSHSLIGWHSTNLGALIVDSCNGL 238

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKL--ETRNMGLKPESYETYQIVDPGEIVFRF--- 295
                R+     E  IL L+     Q++    R + L  +    Y + +   +V R    
Sbjct: 239 AK---RQGLNGNEITILRLADFKDAQRIIGNERKIKLDSKEENKYSLENDDILVIRVNGS 295

Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMG----S 351
            DL       +S   +E        + +  + I S +L ++    +    FY       S
Sbjct: 296 ADLAGRFIEYKSNGDIEGFCDHFIRLRLDSNKIMSRFLTYIANEGE--GRFYLRNSLSTS 353

Query: 352 GLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFI 411
             + ++    +K L  L+PP+KEQ +I   +    A  D + +++  ++  +     S +
Sbjct: 354 AGQNTINQTSIKGLSFLLPPLKEQAEIVRRVEQLFAYADTIEKQVNNALTRVNSLTQSIL 413

Query: 412 AAAVTGQI 419
           A A  G++
Sbjct: 414 AKAFRGEL 421


>gi|77164669|ref|YP_343194.1| restriction modification system DNA specificity subunit
           [Nitrosococcus oceani ATCC 19707]
 gi|254434340|ref|ZP_05047848.1| Type I restriction modification DNA specificity domain protein
           [Nitrosococcus oceani AFC27]
 gi|76882983|gb|ABA57664.1| Restriction modification system DNA specificity domain
           [Nitrosococcus oceani ATCC 19707]
 gi|207090673|gb|EDZ67944.1| Type I restriction modification DNA specificity domain protein
           [Nitrosococcus oceani AFC27]
          Length = 407

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 87/405 (21%), Positives = 178/405 (43%), Gaps = 84/405 (20%)

Query: 21  IPKHWKVVPIKRF---TKLNTGRTSESGKDIIYIGLEDVESGT----------------G 61
           +P+ WK++P+ +    ++  T   S    +   +G++D+++G                  
Sbjct: 16  LPRGWKLLPVGKALIDSQYGTNAASVDAGNTPVVGMKDIQAGKVLTSNLVRANLSDKERA 75

Query: 62  KYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP--KDV 119
           KYL + G+   + T++         L GK+G Y      +D +   ++  + L+     V
Sbjct: 76  KYLLEKGDILINRTNSFD-------LVGKVGIY-----DSDIEAAFASYLVRLKADLSQV 123

Query: 120 LPELLQGWL---LSIDVTQRI--EAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKI 174
           +PE L  WL   ++    +RI  +AI + A ++  ++K   +  +P+P + EQ   RE +
Sbjct: 124 MPEYLNYWLNGHVAQTTIKRIATKAISQ-ANVNPTEFKK--HCYIPLPSIGEQ---REAV 177

Query: 175 IAETVRIDTLITERI-RFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWE 233
               ++ +  + E+I R I   +++ ++L+  ++ K                 L P H++
Sbjct: 178 --SVLKTNDRVIEKIERLIAAKQKRFKSLIQQLINKNCE--------------LWP-HFK 220

Query: 234 VKPFFALVTELNRKNTKLI----ESNILSLSYGNIIQKLETRNMGLKPE-SYETYQIVDP 288
            +  F  ++     N KL+    +  +L  +       LE R M   PE S + Y++V P
Sbjct: 221 ARDLFRNISIKGYGNEKLLSVTQDCGVLPRTM------LEGRVMS--PEGSTDNYKLVVP 272

Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-IDSTYLAWLMRSYDLCKVFY 347
           G  V   I L++ +  L  ++   +GI++ AY  + P   I   +     +SY   + + 
Sbjct: 273 GNFV---ISLRSFQGGLEYSKY--KGIVSPAYTILFPKKEIHDDFYRHFFKSYIFIEKYL 327

Query: 348 AMGS-GLR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARI 389
            +   G+R  + +   D + + +  PP++EQ  I  ++N  T  I
Sbjct: 328 VIAVVGIRDGKQISSSDFESVKIPYPPVQEQRYIAEILNTATEEI 372


>gi|146281027|ref|YP_001171180.1| type I restriction-modification system, S subunit [Pseudomonas
           stutzeri A1501]
 gi|145569232|gb|ABP78338.1| type I restriction-modification system, S subunit [Pseudomonas
           stutzeri A1501]
          Length = 472

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 94/455 (20%), Positives = 182/455 (40%), Gaps = 71/455 (15%)

Query: 18  IGAIPKHWKVVPIKRFTKLNTGRTSE-------SGKDIIYIGLEDVESGTGKYLPKDGNS 70
           +  +P  W    +K    L+ G+T         S +D+ ++  +D++    K L +D   
Sbjct: 1   MSELPSGWTRFALKDLGGLSGGKTPSKANPEFWSTRDVPWVSPKDMK----KNLLEDAED 56

Query: 71  RQS----DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGI---CSTQFLVLQP-KDVLPE 122
           R S    D + ++++  G +L       L+        G+    +    VL+P + ++P+
Sbjct: 57  RISQNAVDEAGMTLYPSGSVLMVTRSGILQHTFPVALAGVELTVNQDIKVLRPIEGIVPK 116

Query: 123 LLQGWLLSIDVTQRIEAIC--EGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVR 180
                L S      I + C  +G T+   D + +      +PPLAEQ  I +K+     +
Sbjct: 117 FSFYMLKSFGA--EILSACSKDGTTVQSIDSEKLETFLFSLPPLAEQTRIAQKLDELLAQ 174

Query: 181 IDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           +DTL         LLK  +Q++++  V+  L           EW G +P     + + + 
Sbjct: 175 VDTLKARIDAIPALLKRFRQSVLAAAVSGRLTE---------EWRGSIPASESAEEYLSR 225

Query: 241 VTELNRKNTKL---------IESNILSLSYGNII-------QKLETRNMGLKPESYETYQ 284
           V ++ R+   +         +E+  L +  G I+       + L++  + +K E  E+ +
Sbjct: 226 VIQVRRQKPIVKFKEPVPPDLETRELEVPEGWIVASVSSFAECLDSMRVPVKKELRESGE 285

Query: 285 IVDP-----GEI--VFRFIDLQNDKRSLRSAQVMERGIITSAY------------MAVKP 325
              P     GE+  V  +I   +D   +   +     +   AY             A++ 
Sbjct: 286 GKYPYFGANGEVDRVDEYI-FDDDLVLVTEDETFYGRVKPIAYKYSGKCWVNNHVHALRA 344

Query: 326 H-GIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINV 384
           H  +   YL +++  YD+  V +  G+  R  L    +  LP+ VPP  EQ +I   +  
Sbjct: 345 HDAVARDYLCYVLMHYDV--VPWLTGTTGRAKLTQGALLSLPIQVPPATEQTEIVRRVEQ 402

Query: 385 ETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQI 419
             A  D L  ++  +   +     S +A A  G++
Sbjct: 403 LFAFADQLEARVNAAKACIDRLTQSILAKAFRGEL 437


>gi|295394613|ref|ZP_06804832.1| type I restriction-mod [Brevibacterium mcbrellneri ATCC 49030]
 gi|294972506|gb|EFG48362.1| type I restriction-mod [Brevibacterium mcbrellneri ATCC 49030]
          Length = 388

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/184 (23%), Positives = 85/184 (46%), Gaps = 12/184 (6%)

Query: 232 WEVKPFFALVTELNRKNTKLIESNILSL--SYGNIIQKLETRNMGLKPESYETYQIVDPG 289
           W+  PF  L   +  K T      +LS+   YG +I+K +  +   +P +   YQ+V  G
Sbjct: 4   WQSVPFHTLFRRVP-KRTGFPAEELLSVYREYG-VIRKSDRDDNFNRPGNLNDYQLVKTG 61

Query: 290 EIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSYDLCKVFYA 348
           ++V   +        +        GI++ AY    P    D ++L + +R  D    + A
Sbjct: 62  DLVLNKMKAWQGSLGISP----HTGIVSPAYFVYTPVSDNDESFLHYALRCRDAVDYYAA 117

Query: 349 MGSGLRQS---LKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKE 405
             +G+R +   +  E +  +PV VP +  Q  I + ++ E + ++ L+E++++   L+  
Sbjct: 118 HSTGIRVNQWDVSPEWLDAMPVPVPDLATQRRIVDYLDKEISEMNALIEEVQRLTKLVIA 177

Query: 406 RRSS 409
           RR +
Sbjct: 178 RRDA 181



 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 128 LLSIDVTQR-IEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLIT 186
            L  DV +R IE    G+T+   +   I  +P P+  L +Q  I +++  E +R+D+LI 
Sbjct: 302 FLGSDVIKRTIEMSTVGSTLKRINVGTIKKLPYPVATLEKQREIADELDREFMRMDSLIE 361

Query: 187 ERIRFIELLKEKKQALVSYIVT 208
           E  R IE LK  K AL++ +VT
Sbjct: 362 ESTRLIENLKAHKTALITEVVT 383



 Score = 46.6 bits (109), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 91/414 (21%), Positives = 165/414 (39%), Gaps = 52/414 (12%)

Query: 25  WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGN-SRQSDTSTVSIFAK 83
           W+ VP     +    RT    ++++ +  E    G  +   +D N +R  + +   +   
Sbjct: 4   WQSVPFHTLFRRVPKRTGFPAEELLSVYRE---YGVIRKSDRDDNFNRPGNLNDYQLVKT 60

Query: 84  GQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWLLSIDVTQRIEAICE 142
           G ++  K+  +     I+   GI S  + V  P  D     L   L   D      A   
Sbjct: 61  GDLVLNKMKAWQGSLGISPHTGIVSPAYFVYTPVSDNDESFLHYALRCRDAVDYYAAHST 120

Query: 143 GATMSHAD----WKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK 198
           G  ++  D    W  +  +P+P+P LA Q  I + +  E   ++ LI E  R  +L+  +
Sbjct: 121 GIRVNQWDVSPEW--LDAMPVPVPDLATQRRIVDYLDKEISEMNALIEEVQRLTKLVIAR 178

Query: 199 KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV-KPFFALVTELNRKNTKLIESNIL 257
           + A    ++       V M    I+ + +     EV   F   + +L  +N  L  +N  
Sbjct: 179 RDATAGSLLADLPVAPVSMFWRVIDCLHITAPFVEVGTNFLVSIEQLGHRNLDLTRANRT 238

Query: 258 SLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGII- 316
                +I+     R    KP          PG+++             R+A V +  I+ 
Sbjct: 239 DDETFSIL-----RVGDRKPA---------PGDVIMS-----------RNASVGKCSIVR 273

Query: 317 -TSAYMAV--------KPHGIDSTYLAWLMRSYDLCKVFYAM---GSGLRQSLKFEDVKR 364
            T   +A+        K    DS  L   + S D+ K    M   GS L++ +    +K+
Sbjct: 274 ETDPPIALGQDVVIFKKNDKHDSRLLLHFLGS-DVIKRTIEMSTVGSTLKR-INVGTIKK 331

Query: 365 LPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQ 418
           LP  V  +++Q +I + ++ E  R+D L+E+  + I  LK  +++ I   VTG+
Sbjct: 332 LPYPVATLEKQREIADELDREFMRMDSLIEESTRLIENLKAHKTALITEVVTGR 385


>gi|325690778|gb|EGD32779.1| type I restriction-modification system specificity protein
           [Streptococcus sanguinis SK115]
          Length = 409

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 71/159 (44%), Gaps = 29/159 (18%)

Query: 19  GAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKD--------GNS 70
           G +P  W +  +    KL            I  G+ D +     Y+P D         NS
Sbjct: 213 GKMPNDWTIGKLSDVLKL------------IKNGINDKDKQKLPYVPIDILPMHSLSLNS 260

Query: 71  RQSD---TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGW 127
            +S+    S++  F K  IL G +  Y  +  I+ F GI  +   VL+P + +   L+  
Sbjct: 261 YKSNDEAKSSLITFKKNDILLGAMRVYFHRVCISPFTGITRSTCFVLRPFNKI--YLEYC 318

Query: 128 LLSIDVTQRIE---AICEGATMSHADWK-GIGNIPMPIP 162
           LL+ D+   IE   +  +G+TM +A W+ G+  + +PIP
Sbjct: 319 LLTCDLKSSIEYAQSTSKGSTMPYAVWENGLAELKIPIP 357


>gi|191639030|ref|YP_001988196.1| HsdS [Lactobacillus casei BL23]
 gi|190713332|emb|CAQ67338.1| HsdS [Lactobacillus casei BL23]
          Length = 190

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/132 (32%), Positives = 61/132 (46%), Gaps = 8/132 (6%)

Query: 40  RTSESGKD--IIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQ-ILYGKLGPYLR 96
           R +++  D  I  +  ED+ S  G+ L KD   R    S   I+ + Q +L+GKL PYL+
Sbjct: 26  RVNKTSDDSTIPSVEFEDIISKQGR-LNKD--VRLKINSKQGIYFEPQDVLFGKLRPYLQ 82

Query: 97  KAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIG 155
             +   F G     F VL+    VL E L   L+     Q +  I  G  M  +DW  + 
Sbjct: 83  NWLFPSFYGRAVGDFWVLRANSSVLSEYLFV-LIQSPRFQIVANISSGTKMPRSDWNTVS 141

Query: 156 NIPMPIPPLAEQ 167
           N   PIP  +EQ
Sbjct: 142 NTSFPIPVQSEQ 153


>gi|164551512|gb|ABY60973.1| Sau1hsdS1 [Staphylococcus aureus]
          Length = 394

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 79/374 (21%), Positives = 163/374 (43%), Gaps = 66/374 (17%)

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKA--IIAD-------------FDGIC- 107
           +PK    + SD +       GQ++YGKL  +L  A  I+ D             FD I  
Sbjct: 56  VPKKETFKGSDNTQYYKRKAGQLMYGKL-DFLNCAFGIVPDSLNNYESTIDSPSFDFING 114

Query: 108 STQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQ 167
            ++FL+ + K  L    + +    + +++ + I +   +S         +P+  P   EQ
Sbjct: 115 DSKFLLERIK--LKSFYKKFGDIANGSRKAKRINQDTFLS---------LPVFAPKYDEQ 163

Query: 168 VLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGL 227
           + I E       ++D  I  + + +ELL+++K+  +  I ++    +++ KD      G 
Sbjct: 164 LRIGEFF----SKLDRQIELQKQKLELLQQQKKGYMQKIFSQ----ELRFKDEN----GE 211

Query: 228 VPDHWEVKPFFALVTELNRKNTK------LIESNILSLSYGNIIQKLETRNMGLKPESYE 281
              HWE       + E N ++ K       I S I+  S      +L+ ++   K +S  
Sbjct: 212 DYPHWENSKIEKYLKERNERSDKGQMLSVTINSGIIKFS------ELDRKDNSSKNKS-- 263

Query: 282 TYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKP-HGIDSTYLAWLMRSY 340
            Y++V   +I +  + +        S +    GI++ AY  + P     S ++ +  +++
Sbjct: 264 NYKVVRKNDIAYNSMRMWQGA----SGKSNYNGIVSPAYTVLYPTQNTSSLFIGYKFKTH 319

Query: 341 DLCKVFYAMGSGLRQ---SLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIE 397
            +   F     GL     +LK++ +K + + +P ++EQ  I +       ++D+L+ K +
Sbjct: 320 RMIHKFKINSQGLTSDTWNLKYKQLKNINIDIPVLEEQEKIGDFF----KKMDILISKQK 375

Query: 398 QSIVLLKERRSSFI 411
             I +L++ + SF+
Sbjct: 376 IKIEILEKEKQSFL 389


>gi|15669403|ref|NP_248213.1| type I restriction-modification enzyme 1 subunit S
           [Methanocaldococcus jannaschii DSM 2661]
 gi|2496161|sp|Q58615|Y1218_METJA RecName: Full=Uncharacterized protein MJ1218
 gi|1591847|gb|AAB99219.1| type I restriction-modification enzyme 1, S subunit
           [Methanocaldococcus jannaschii DSM 2661]
          Length = 425

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 70/131 (53%), Gaps = 9/131 (6%)

Query: 105 GICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPP 163
           GI S+  + L+ K+ ++ +L   + L +  +  +++  +G  + H D K   NI +P+PP
Sbjct: 103 GILSSTMVKLEQKNKIMDDLYLFYSLKLKES-FLKSQTKGTGIPHVDKKIFENIKIPLPP 161

Query: 164 LAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIE 223
           L EQ  I  KI+++    D LI    + IE+L + K+ ++  + TKG+      K S I 
Sbjct: 162 LEEQKQIA-KILSD---FDNLIGTINKQIEVLNKAKKGMMKKLFTKGVFEHKSFKKSEI- 216

Query: 224 WVGLVPDHWEV 234
             G +P+ WEV
Sbjct: 217 --GEIPEDWEV 225


>gi|110800744|ref|YP_696988.1| type I restriction-modification enzyme, S subunit [Clostridium
           perfringens ATCC 13124]
 gi|110675391|gb|ABG84378.1| type I restriction-modification enzyme, S subunit [Clostridium
           perfringens ATCC 13124]
          Length = 417

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 97/224 (43%), Gaps = 16/224 (7%)

Query: 18  IGAIPKHWKVVPIKRFTKLNT---GRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSD 74
           +G IP  W+V  I    K+N+      +E    + YI +E V +G    + K     Q+ 
Sbjct: 14  LGEIPNEWEVCRIDDLCKVNSKSLNSKTEPNLVVNYIDIESVSTGKINNI-KQMIFSQAP 72

Query: 75  TSTVSIFAKGQILYGKLGPYLR---KAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLS 130
           +    +  K  ++   + PYL+   K   +  + +CST F VL+  + V  E +   +LS
Sbjct: 73  SRARRVVKKNDVIMSTVRPYLKAFVKVKSSLNNLVCSTGFAVLEVNEGVNSEFVYQSILS 132

Query: 131 IDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIR 190
               ++I+    G+     +   +    + +P + EQ    EKI      +D  I    +
Sbjct: 133 NYFIEQIKNKMVGSNYPAVNSDDVKESKLILPSIQEQ----EKIAEILSTVDEQIENTEK 188

Query: 191 FIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEV 234
            I+  +E K+ L+  ++TKG+      K      +G +P  W++
Sbjct: 189 LIQKNQELKKGLMQQLLTKGIGHTEFKKTE----LGYIPKEWKI 228


>gi|312902064|ref|ZP_07761325.1| type I restriction modification DNA specificity domain protein
           [Enterococcus faecalis TX0470]
 gi|311290846|gb|EFQ69402.1| type I restriction modification DNA specificity domain protein
           [Enterococcus faecalis TX0470]
          Length = 380

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 84/356 (23%), Positives = 144/356 (40%), Gaps = 63/356 (17%)

Query: 74  DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQP-KDVLPELLQGWLLSID 132
           + S+  I  KG ILY   G    +  I+  +G  +   L ++P K+  P L+  WLL   
Sbjct: 48  NNSSAKIVEKGDILYALYGATSGEVGISQINGAINQAILAIRPIKEDEPYLIAQWLL--- 104

Query: 133 VTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTL-------I 185
             ++ E+I            G GN+   I  + E VL   K  AE  +I T        I
Sbjct: 105 --KQKESIIRTYLQG-----GQGNLSSSI--VKELVLKLPKDKAEQAKIGTFFKQLDDTI 155

Query: 186 TERIRFIELLKEKKQAL--VSYIVTKGLN---PDVKMKDSGIEWVGLVPDHWEVKPFFAL 240
           T   R +E LKE K A   V ++  K  N   P ++  D G EW     D  + K  F  
Sbjct: 156 TLHQRKLEQLKELKTAYLQVMFVSMKTKNNKVPKLRFADFGGEW-----DQRKSKELFIP 210

Query: 241 VTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQN 300
            +E N+ N  ++    ++   G + +     ++     S + Y++V+  + V        
Sbjct: 211 KSEKNQPNLPVLS---VTQDSGVVYRDQVGIDINYDLTSLKNYKVVNKNDFVI------- 260

Query: 301 DKRSLRSAQ-----VMERGIITSAYMAVKPHGI---DSTYLAWLMRSYDLCKVFYAMGSG 352
              SLRS Q       ++GI + AY    P  I   D+ +     +++   +    +  G
Sbjct: 261 ---SLRSFQGGFELSDKKGITSPAYTIFVPKDIKLHDNLFWKTQFKTFQFIEALKTVTFG 317

Query: 353 LR--QSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
           +R  +S+ F +   L +  P  K+          E  +I    E+++ +I L + +
Sbjct: 318 IRDGKSISFTEFGDLKLCFPKNKK----------EQQKIGKFFEELDYAISLHQNK 363


>gi|322517064|ref|ZP_08069949.1| hypothetical protein HMPREF9425_1226 [Streptococcus vestibularis
           ATCC 49124]
 gi|322124324|gb|EFX95832.1| hypothetical protein HMPREF9425_1226 [Streptococcus vestibularis
           ATCC 49124]
          Length = 381

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 35/119 (29%), Positives = 57/119 (47%), Gaps = 3/119 (2%)

Query: 75  TSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSID-V 133
           T  V+ F K  IL   + PYL+K   AD DG  S+  LV++P DV+      + L+ D  
Sbjct: 46  TQKVTRFKKNDILIANIRPYLKKIWQADIDGGASSDVLVVRPNDVIDYNFLYYALTQDSF 105

Query: 134 TQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE--KIIAETVRIDTLITERIR 190
            + +    +G  M   D   I N  +P   + EQ+ I +  K I + ++I+  I + + 
Sbjct: 106 FEYVMKGSKGTKMPRGDKSQIMNFVIPDLEIDEQIKIGKLLKSIDQKIQINNQINQELE 164


>gi|163784829|ref|ZP_02179613.1| type I restriction-modification system specificity subunit
           [Hydrogenivirga sp. 128-5-R1-1]
 gi|159879899|gb|EDP73619.1| type I restriction-modification system specificity subunit
           [Hydrogenivirga sp. 128-5-R1-1]
          Length = 80

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query: 347 YAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKER 406
           +  GS  ++ +  E VK L + +PP+ EQ  I   ++ +T +ID L++K E+ I L+KE 
Sbjct: 6   FMTGSAGQKRIPTEFVKNLQIPLPPLHEQQKIAQYLDKKTQQIDQLIQKTEKEIKLIKEF 65

Query: 407 RSSFIAAAVTGQI 419
           +   I+ AV G+I
Sbjct: 66  KEKLISDAVLGKI 78



 Score = 37.7 bits (86), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 35/54 (64%)

Query: 154 IGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIV 207
           + N+ +P+PPL EQ  I + +  +T +ID LI +  + I+L+KE K+ L+S  V
Sbjct: 21  VKNLQIPLPPLHEQQKIAQYLDKKTQQIDQLIQKTEKEIKLIKEFKEKLISDAV 74


>gi|327383090|gb|AEA54566.1| hypothetical protein LC2W_2234 [Lactobacillus casei LC2W]
          Length = 608

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/158 (31%), Positives = 68/158 (43%), Gaps = 10/158 (6%)

Query: 51  IGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQ-ILYGKLGPYLRKAIIADFDGICST 109
           +  ED+ S  G+ L KD   R    S   I+ + Q +L+GKL PYL+  +   F G    
Sbjct: 245 VEFEDIISKQGR-LNKD--VRLKINSKQGIYFEPQDVLFGKLRPYLQNWLFPSFYGRAVG 301

Query: 110 QFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQV 168
            F VL+    VL E L   L+     Q +  I  G  M  +DW  + N   PIP  +EQ 
Sbjct: 302 DFWVLRANSSVLSEYL-FVLIQSPRFQIVANISSGTKMPRSDWNTVSNTSFPIPVQSEQ- 359

Query: 169 LIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYI 206
               KI      +D LI      +  LK+ K   +  I
Sbjct: 360 ---RKIWQLFNVLDNLIAATQDKLSFLKKMKMFFLQQI 394


>gi|312128027|ref|YP_003992901.1| restriction modification system DNA specificity domain-containing
           protein [Caldicellulosiruptor hydrothermalis 108]
 gi|311778046|gb|ADQ07532.1| restriction modification system DNA specificity domain protein
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 433

 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 101/455 (22%), Positives = 198/455 (43%), Gaps = 79/455 (17%)

Query: 2   KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTG 61
           K+YK    +KDS    +G IP+ W+VV +    K+ TG ++           +  E+G  
Sbjct: 7   KNYK----FKDSP---LGRIPEEWEVVRLGDIAKIKTGNSNVQ---------DAAETGDY 50

Query: 62  KYLPKDGNSRQS-----DTSTVSIFAKG-----QILYGKLGPYLRKAIIADFDGICSTQF 111
            +  + G  ++S     D   V +  +G     +   GK   + R   I DF  + S ++
Sbjct: 51  LFFDRSGEIKRSNRYLFDKEAVIVPGEGTEFLPKYYCGKFDLHQRAYAIFDFSSVLSGEY 110

Query: 112 LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIR 171
           L          +L  W +             G T+         N+ + +PPL