RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6471
(635 letters)
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 68.2 bits (167), Expect = 4e-13
Identities = 38/129 (29%), Positives = 61/129 (47%), Gaps = 10/129 (7%)
Query: 506 FTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREI 565
F A L++ L E E L S DL+S+E L+ +H+ E+ +L E
Sbjct: 5 FLRDADELEAWLSEKEELLSS---TDYGDDLESVEALLKKHEALEA-------ELAAHEE 54
Query: 566 QFSAVQDRGEALILQHHPAAKCIEAYMAAMQSQWAWLLQLALCLETHLKHAAYYHQFWRE 625
+ A+ + GE LI + HP A+ I+ + + +W L +LA L+ A QF+R+
Sbjct: 55 RVEALNELGEQLIEEGHPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQQFFRD 114
Query: 626 MKDAETWIN 634
D E W+
Sbjct: 115 ADDLEQWLE 123
Score = 52.4 bits (126), Expect = 1e-07
Identities = 57/215 (26%), Positives = 101/215 (46%), Gaps = 37/215 (17%)
Query: 396 AQIQEADYGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALN 455
+ DYG DL+ V+A + H+ + + RVE ALN
Sbjct: 21 ELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVE--------------------ALN 60
Query: 456 EDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARA-EEDMKNATKL--FTEKASN 512
E ++L+EEG P +++ ++E+N+ ++E A + ++ A L F A +
Sbjct: 61 ELGEQLIEEGHPDAEEIQE---RLEELNQRWEELRELAEERRQRLEEALDLQQFFRDADD 117
Query: 513 LQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQD 572
L+ L+E E L S + +DL+S+E L+ +HK+ E +LE E + ++ +
Sbjct: 118 LEQWLEEKEAALASE---DLGKDLESVEELLKKHKELEE-------ELEAHEPRLKSLNE 167
Query: 573 RGEALILQHHPAA-KCIEAYMAAMQSQWAWLLQLA 606
E L+ + HP A + IE + + +W LL+LA
Sbjct: 168 LAEELLEEGHPDADEEIEEKLEELNERWEELLELA 202
Score = 50.1 bits (120), Expect = 6e-07
Identities = 37/186 (19%), Positives = 69/186 (37%), Gaps = 29/186 (15%)
Query: 218 LAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLF 277
++ R+ ++ L E E ++ D + LE +L EE + L
Sbjct: 1 KLQQFLRDADELEAWLSEKEELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVEALN 60
Query: 278 SDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQT 337
+ L E +P A ++ +R+++L+QRW LR L R
Sbjct: 61 ELGEQLIEEGHPDAEEIQERLEELNQRWEELRELAEER---------------------- 98
Query: 338 RTVMETRLVDTN---THFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNI 394
RL + FR + +W++ K A + D G DL+ V+ + H+ +
Sbjct: 99 ----RQRLEEALDLQQFFRDADDLEQWLEEKEAALASEDLGKDLESVEELLKKHKELEEE 154
Query: 395 IAQIQE 400
+ +
Sbjct: 155 LEAHEP 160
Score = 37.8 bits (88), Expect = 0.008
Identities = 37/215 (17%), Positives = 83/215 (38%), Gaps = 15/215 (6%)
Query: 103 EYCDLASSLHLWMREKTAYMQDRNFPSTLIEMKKLAADSARFRTEEVPPRQRDKQRLQHI 162
++ A L W+ EK + ++ L ++ L E ++R++ +
Sbjct: 4 QFLRDADELEAWLSEKEELLSSTDYGDDLESVEALLKKHEALEAEL----AAHEERVEAL 59
Query: 163 FQDLTKYFEDVGEVDIDP-ELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEK 221
+L + + G D + + ++ + + W L +E+ L++ +
Sbjct: 60 -NELGEQLIEEGHPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQQFF------ 112
Query: 222 VTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQ 281
R+ ++ LEE E+ + E D + LE +L E + +L +
Sbjct: 113 --RDADDLEQWLEEKEAALASEDLGKDLESVEELLKKHKELEEELEAHEPRLKSLNELAE 170
Query: 282 TLRE-GRYPQASDLHKRVQKLHQRWVALRSLLHSR 315
L E G ++ +++++L++RW L L R
Sbjct: 171 ELLEEGHPDADEEIEEKLEELNERWEELLELAEER 205
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 53.5 bits (129), Expect = 5e-09
Identities = 34/109 (31%), Positives = 57/109 (52%), Gaps = 10/109 (9%)
Query: 506 FTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREI 565
F A L++ L+E E+ L S + +DL+S+E L+ +H+ FE+ +LE E
Sbjct: 3 FLRDADELEAWLEEKEQLLASE---DLGKDLESVEALLKKHEAFEA-------ELEAHEE 52
Query: 566 QFSAVQDRGEALILQHHPAAKCIEAYMAAMQSQWAWLLQLALCLETHLK 614
+ A+ + GE LI + HP A+ IE + + +W L +LA L+
Sbjct: 53 RVEALNELGEQLIEEGHPDAEEIEERLEELNERWEELKELAEERRQKLE 101
Score = 36.5 bits (85), Expect = 0.006
Identities = 23/92 (25%), Positives = 41/92 (44%)
Query: 224 REMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTL 283
R+ ++ LEE E + E D + E +L EE + L + L
Sbjct: 5 RDADELEAWLEEKEQLLASEDLGKDLESVEALLKKHEAFEAELEAHEERVEALNELGEQL 64
Query: 284 REGRYPQASDLHKRVQKLHQRWVALRSLLHSR 315
E +P A ++ +R+++L++RW L+ L R
Sbjct: 65 IEEGHPDAEEIEERLEELNERWEELKELAEER 96
Score = 32.3 bits (74), Expect = 0.14
Identities = 12/49 (24%), Positives = 22/49 (44%)
Query: 352 FRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQE 400
R E W++ K + D G DL+ V+A + H+ + + +E
Sbjct: 4 LRDADELEAWLEEKEQLLASEDLGKDLESVEALLKKHEAFEAELEAHEE 52
Score = 29.2 bits (66), Expect = 2.1
Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 23/100 (23%)
Query: 396 AQIQEADYGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALN 455
+ D G DL+ V+A + H+ + +E RV +ALN
Sbjct: 19 QLLASEDLGKDLESVEALLKKHEAFEAELEAHEERV--------------------EALN 58
Query: 456 EDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARA 495
E ++L+EEG P + + ++E+N ++E + A
Sbjct: 59 ELGEQLIEEGHPDAEE---IEERLEELNERWEELKELAEE 95
>gnl|CDD|215918 pfam00435, Spectrin, Spectrin repeat. Spectrin repeat-domains are
found in several proteins involved in cytoskeletal
structure. These include spectrin, alpha-actinin and
dystrophin. The sequence repeat used in this family is
taken from the structural repeat in reference. The
spectrin domain- repeat forms a three helix bundle. The
second helix is interrupted by proline in some
sequences. The repeats are defined by a characteristic
tryptophan (W) residue at position 17 in helix A and a
leucine (L) at 2 residues from the carboxyl end of helix
C. Although the domain occurs in ultiple repeats along
sequences, the domains are actually stable on their own
- ie they act, biophysically, like domains rather than
repeats that along function when aggregated.
Length = 105
Score = 45.4 bits (108), Expect = 5e-06
Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 10/101 (9%)
Query: 506 FTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREI 565
F A +L+S ++E E L S +DL+S++ L+ +HK E+ +L +
Sbjct: 6 FFRDADDLESWIEEKEALLSSE---DYGKDLESVQALLKKHKALEA-------ELAAHQD 55
Query: 566 QFSAVQDRGEALILQHHPAAKCIEAYMAAMQSQWAWLLQLA 606
+ A+ + E LI + H A++ I+ + + +W LL+LA
Sbjct: 56 RVEALNELAEKLIAEGHYASEEIQERLEELNERWEQLLELA 96
Score = 33.8 bits (78), Expect = 0.045
Identities = 20/102 (19%), Positives = 43/102 (42%), Gaps = 4/102 (3%)
Query: 214 RLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENI 273
LQ+ ++ + L S + + L+ + L KH LE +L ++ +
Sbjct: 2 LLQQFFRDADDLESWIEEKEALLSSE--DYGKDLESVQALLKKH--KALEAELAAHQDRV 57
Query: 274 NTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSR 315
L + L + + ++ +R+++L++RW L L R
Sbjct: 58 EALNELAEKLIAEGHYASEEIQERLEELNERWEQLLELAAER 99
Score = 33.4 bits (77), Expect = 0.077
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 352 FRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQE-----ADYGSD 406
FR + W++ K A + DYG DL+ VQA + H+ + +A Q+ +
Sbjct: 7 FRDADDLESWIEEKEALLSSEDYGKDLESVQALLKKHKALEAELAAHQDRVEALNELAEK 66
Query: 407 LQ--GVQAEIAIHQREQNIIEQF 427
L G A I +R + + E++
Sbjct: 67 LIAEGHYASEEIQERLEELNERW 89
Score = 32.3 bits (74), Expect = 0.16
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 23/104 (22%)
Query: 392 QNIIAQIQEADYGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIR 451
+ A + DYG DL+ VQA + H+ + + RVE
Sbjct: 18 EEKEALLSSEDYGKDLESVQALLKKHKALEAELAAHQDRVE------------------- 58
Query: 452 KALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARA 495
ALNE A+KL+ EG + + ++ ++E+N +++ A
Sbjct: 59 -ALNELAEKLIAEGHYASEE---IQERLEELNERWEQLLELAAE 98
Score = 29.2 bits (66), Expect = 1.9
Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 4/100 (4%)
Query: 108 ASSLHLWMREKTAYMQDRNFPSTLIEMKKLAADSARFRTEEVPPRQRDKQRLQHIFQDLT 167
A L W+ EK A + ++ L ++ L E+ Q + L + + L
Sbjct: 10 ADDLESWIEEKEALLSSEDYGKDLESVQALLKKHKALE-AELAAHQDRVEALNELAEKLI 68
Query: 168 KYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQD 207
+I + ++ + W +LL E+ L++
Sbjct: 69 AE-GHYASEEI--QERLEELNERWEQLLELAAERKQKLEE 105
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 48.9 bits (117), Expect = 8e-06
Identities = 59/349 (16%), Positives = 125/349 (35%), Gaps = 40/349 (11%)
Query: 224 REMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTL 283
RE++ ++ ++EELE +I E + L L ++ LR+ E ++ S ++
Sbjct: 677 REIEELEEKIEELEEKIAELEKALAEL--RKELEELEEELEQLRKELEELSRQISALRK- 733
Query: 284 REGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMET 343
+ L V++L +R L +E T +E
Sbjct: 734 ------DLARLEAEVEQLEERIAQLS-------------------KELTELEAEIEELEE 768
Query: 344 RLVDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQE--A 401
RL + + IE ++ ++ Q++E ++A + + + E A
Sbjct: 769 RLEEAEEELAEAEAEIEELEAQIEQLKEE--------LKALREALDELRAELTLLNEEAA 820
Query: 402 DYGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKL 461
+ L+ ++ IA +R +E+ + I + + + + L + + L
Sbjct: 821 NLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEEL--IEELESELEAL 878
Query: 462 LEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASNLQSKLDEAE 521
L E + L LR E++E++ E E + + + L+
Sbjct: 879 LNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRI 938
Query: 522 RTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAV 570
L R++ L+ E L + +D E + + LE + + V
Sbjct: 939 DNLQERLSEEYSLTLEEAEALENKIEDDEEEARRRLKRLENKIKELGPV 987
Score = 46.6 bits (111), Expect = 4e-05
Identities = 75/359 (20%), Positives = 148/359 (41%), Gaps = 57/359 (15%)
Query: 210 KRLDRLQRLAEKVTREMKRVDGRLEELE-----SRINEEARRLDRLHPLDAKHNVDVLEH 264
++L L+R AEK R K + L ELE R+ E L+ L + + E
Sbjct: 200 RQLKSLERQAEKAER-YKELKAELRELELALLVLRLEELREELEEL-----QEELKEAEE 253
Query: 265 DLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMS 324
+L + + L ++ LR L + +++L + AL + + SRL +
Sbjct: 254 ELEELTAELQELEEKLEELRLEVSE----LEEEIEELQKELYALANEI-SRLEQQKQILR 308
Query: 325 FPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAE 384
E + +E +L + + L E + ++ KL +++E +L+ ++AE
Sbjct: 309 ----ERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKE-----ELESLEAE 359
Query: 385 IA-IHQREQNIIAQIQEADYGSDLQGVQAEIAIHQREQNI----IEQFHTRVEHCIAAKF 439
+ + + + ++++E + L+ +++++A + + IE+ R+E
Sbjct: 360 LEELEAELEELESRLEELE--EQLETLRSKVAQLELQIASLNNEIERLEARLER------ 411
Query: 440 LAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNR-LFDEFERRARAEED 498
R + E+ K LEE +L+ L+ E++E+ L + E R EE
Sbjct: 412 ----LEDRRERLQQEIEELLKKLEE-----AELKELQAELEELEEELEELQEELERLEEA 462
Query: 499 MKNATKLFTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLM 557
++ + E L + E + L +R LDSLE L + F +K L+
Sbjct: 463 LEELREELEEAEQALDAAERELAQ-LQAR--------LDSLERLQENLEGFSEGVKALL 512
Score = 46.2 bits (110), Expect = 5e-05
Identities = 58/359 (16%), Positives = 129/359 (35%), Gaps = 57/359 (15%)
Query: 137 LAADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSRLLA 196
L EE+ Q + + + ++LT + +E L
Sbjct: 229 LLVLRLEELREELEELQEELKEAEEELEELTA--------------ELQELEEKLEELRL 274
Query: 197 AHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRL--HPLD 254
E + +++ K L L ++ ++ + + RL LE ++ E +L+ L +
Sbjct: 275 EVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDE 334
Query: 255 AKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHS 314
+ LE L + +E + +L ++++ L + +L R+++L ++ LRS +
Sbjct: 335 LAEELAELEEKLEELKEELESLEAELEELEA----ELEELESRLEELEEQLETLRSKVAQ 390
Query: 315 RLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEADY 374
+ +E RL LQ+ IE + KL + + +
Sbjct: 391 LE------------LQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKEL 438
Query: 375 GSDLQGVQAEIA--------IHQREQNIIAQIQEA-----DYGSDLQGVQAEIAIHQREQ 421
++L+ ++ E+ + + + + +++EA +L +QA + +R Q
Sbjct: 439 QAELEELEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDSLERLQ 498
Query: 422 NIIEQFHTRVEHCIAAKFLAMGAAQR------------NAIRKALNEDADKLLEEGDPS 468
+E F V+ + + G AI AL ++ E +
Sbjct: 499 ENLEGFSEGVKALLKNQSGLSGILGVLSELISVDEGYEAAIEAALGGRLQAVVVENLNA 557
Score = 36.6 bits (85), Expect = 0.051
Identities = 52/333 (15%), Positives = 119/333 (35%), Gaps = 45/333 (13%)
Query: 181 ELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRI 240
EL + ++ L +E L++ + L+ L +++ +++ + + ELE I
Sbjct: 224 ELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEI 283
Query: 241 NEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQK 300
E + L + + LE + E + L ++ L S L + ++
Sbjct: 284 EELQKEL-----YALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEE 338
Query: 301 LHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIE 360
L + L L EE +E L + + L+E +E
Sbjct: 339 LAELEEKLEELK----------------EELESLEAELEELEAELEELESRLEELEEQLE 382
Query: 361 WVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIAIHQRE 420
+++K+AQ++ + ++ +I+ + + L+ ++ Q+E
Sbjct: 383 TLRSKVAQLE------------------LQIASLNNEIERLE--ARLERLEDRRERLQQE 422
Query: 421 QNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMD 480
+ + E K L + + L E+ ++L E + +L + +D
Sbjct: 423 IEELLKKLEEAE----LKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALD 478
Query: 481 EVNRLFDEFERRARAEEDMKNATKLFTEKASNL 513
R + + R + E ++ + F+E L
Sbjct: 479 AAERELAQLQARLDSLERLQENLEGFSEGVKAL 511
Score = 36.2 bits (84), Expect = 0.056
Identities = 48/305 (15%), Positives = 101/305 (33%), Gaps = 62/305 (20%)
Query: 199 QEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHN 258
+E + + + L RL +V + +R+ +EL E +RL + +
Sbjct: 719 KELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEE-- 776
Query: 259 VDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVS 318
L +AE I L + ++ L+E + L + + +L L
Sbjct: 777 -------LAEAEAEIEELEAQIEQLKE----ELKALREALDELRAELTLLN--------- 816
Query: 319 PLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLA---------QI 369
EE R+ +E R+ T L+E IE + + +
Sbjct: 817 ----------EEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEE 866
Query: 370 QEADYGSDLQGVQAEIAIHQ--------REQNIIAQIQEADYGSDLQGVQAEIAIHQREQ 421
+ S+L+ + E A + + + +++E + + +
Sbjct: 867 LIEELESELEALLNERASLEEALALLRSELEELSEELRELE-----SKRSELRRELEELR 921
Query: 422 NIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQ-----LRRLR 476
+ Q R+E + +R + +L + + LE D + L+RL
Sbjct: 922 EKLAQLELRLE---GLEVRIDNLQERLSEEYSLTLEEAEALENKIEDDEEEARRRLKRLE 978
Query: 477 REMDE 481
++ E
Sbjct: 979 NKIKE 983
Score = 33.5 bits (77), Expect = 0.42
Identities = 46/238 (19%), Positives = 83/238 (34%), Gaps = 25/238 (10%)
Query: 137 LAADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSRLLA 196
EV + +L +L E++ E + E + E L A
Sbjct: 730 ALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEA 789
Query: 197 AHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPL--D 254
++ L+ + LD L+ + E + RLE LE RI RRL+ L +
Sbjct: 790 QIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEE 849
Query: 255 AKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHS 314
+++ L ++ + EE I L S+++ L L + LRS L
Sbjct: 850 LSEDIESLAAEIEELEELIEELESELE-----------ALLNERASLEEALALLRSELEE 898
Query: 315 RLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEA 372
+ EE R+ + L + L+ +E ++ ++ +QE
Sbjct: 899 ------------LSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQER 944
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 46.2 bits (110), Expect = 5e-05
Identities = 67/381 (17%), Positives = 153/381 (40%), Gaps = 50/381 (13%)
Query: 155 DKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDR 214
K+ L+ + ++L + + ++ E + ++ L +E L++ ++L+
Sbjct: 665 QKRELKELEEELAELEAQLEKL----EEELKSLKNELRSLEDLLEELRRQLEELERQLEE 720
Query: 215 LQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENIN 274
L+R + E++++ RLEELE + E L+ L + ++ LE +L EE +
Sbjct: 721 LKRELAALEEELEQLQSRLEELEEELEELEEELEEL-----QERLEELEEELESLEEALA 775
Query: 275 TLFSDVQTLREGRYPQAS---DLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEER 331
L +++ L E R +L + +++ +R AL L S + R
Sbjct: 776 KLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLE------------QRR 823
Query: 332 TVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQRE 391
Q +E + + L+E +E ++ +L +++E +L+ ++AE + E
Sbjct: 824 ERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKE-----ELEELEAEKE--ELE 876
Query: 392 QNII-AQIQEADYGSDLQGVQAEIA-IHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNA 449
+ + ++ + +L+ +++E+A + + + + E+ +
Sbjct: 877 DELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKL--ERLEVEL---PEL 931
Query: 450 IRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRL-FDEFERRARAEEDMKNATKLFTE 508
+ E D L E + +L + VN +E+E E++K
Sbjct: 932 EEELEEEYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYEELK-------- 983
Query: 509 KASNLQSKLDEAERTLHSRIN 529
+ + L+EA+ L I
Sbjct: 984 ---SQREDLEEAKEKLLEVIE 1001
Score = 45.9 bits (109), Expect = 6e-05
Identities = 66/372 (17%), Positives = 152/372 (40%), Gaps = 61/372 (16%)
Query: 210 KRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAK---HNVDVLEHDL 266
++L+R + E++ ++ ++ +LE+LE +A + +R L A+ + +L L
Sbjct: 179 RKLERTEENLERLEDLLEELEKQLEKLE----RQAEKAERYQELKAELRELELALLLAKL 234
Query: 267 RQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFP 326
++ + + L ++ L E + +L + +++ + L+S L
Sbjct: 235 KELRKELEELEEELSRLEE----ELEELQEELEEAEKEIEELKSELEE------------ 278
Query: 327 VVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIA 386
+ L + L+E IE ++ +++ ++E + + + E
Sbjct: 279 --------------LREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEER 324
Query: 387 IHQREQNIIAQIQE-ADYGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAA 445
+ + ++ I A +E + + L+ ++ +A + E+ ++ +
Sbjct: 325 LEELKEKIEALKEELEERETLLEELEQLLAELEE---AKEELEEKLSALLEELE------ 375
Query: 446 QRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKL 505
+ +AL E+ +L E +L L+RE++ L + ER + ED+K K
Sbjct: 376 ---ELFEALREELAELEAELAEIRNELEELKREIES---LEERLERLSERLEDLKEELKE 429
Query: 506 FTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREI 565
+ LQ++L+E L LE L + K+ E L L +L++ E
Sbjct: 430 LEAELEELQTELEELNEELEELEEQ--------LEELRDRLKELERELAELQEELQRLEK 481
Query: 566 QFSAVQDRGEAL 577
+ S+++ R + L
Sbjct: 482 ELSSLEARLDRL 493
Score = 39.7 bits (93), Expect = 0.005
Identities = 54/328 (16%), Positives = 129/328 (39%), Gaps = 43/328 (13%)
Query: 184 IDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEE 243
++ +ER L + L+ RL+ L+ E++ E++ + RLEELE +
Sbjct: 711 LEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESL 770
Query: 244 ARRLDRLHPLDA---------KHNVDVLEHDLRQAEENINTLFSDVQTLREGR---YPQA 291
L +L + ++ LE +L +AE ++ L ++++L + R +
Sbjct: 771 EEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEI 830
Query: 292 SDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTH 351
+L + +++L ++ L L L L + EE + +E L +
Sbjct: 831 EELEEEIEELEEKLDELEEEL-EELEKELEELK----EELEELEAEKEELEDELKELEEE 885
Query: 352 FRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNI-IAQIQEADYGSDLQGV 410
L+E + ++++LA+++E + + + + E + +++ + +L+
Sbjct: 886 KEELEEELRELESELAELKE-------EIEKLRERLEELEAKLERLEVELPELEEELEEE 938
Query: 411 QAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAI--RKALNEDADKLLEEGDPS 468
+ + E+ I + + A+G AI + + E ++L
Sbjct: 939 YEDTLETELEREIER---------LEEEIEALGPVNLRAIEEYEEVEERYEELKS----- 984
Query: 469 DPQLRRLRREMDEVNRLFDEFERRARAE 496
Q L +++ + +E ++ R
Sbjct: 985 --QREDLEEAKEKLLEVIEELDKEKRER 1010
Score = 37.0 bits (86), Expect = 0.036
Identities = 22/118 (18%), Positives = 49/118 (41%), Gaps = 2/118 (1%)
Query: 199 QEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHN 258
++ ++L++ + + L+ ++ E+ + LEEL+ I RL+RL
Sbjct: 365 EKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLK 424
Query: 259 VDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRL 316
++ +L E + T ++ E Q +L R+++L + L+ L
Sbjct: 425 EELK--ELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQEELQRLE 480
Score = 35.8 bits (83), Expect = 0.085
Identities = 33/187 (17%), Positives = 77/187 (41%), Gaps = 9/187 (4%)
Query: 131 LIEMKKLAADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERN 190
L E + + E + + + + L+ L + E++ E + ++ +E
Sbjct: 742 LEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEE 801
Query: 191 WSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRL 250
+ L+ +R +RL++ E++ E++ ++ +L+ELE + E + L+ L
Sbjct: 802 LEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEEL 861
Query: 251 HPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRS 310
K ++ LE + + E+ + L + + L E + +L + +L + LR
Sbjct: 862 -----KEELEELEAEKEELEDELKELEEEKEELEE----ELRELESELAELKEEIEKLRE 912
Query: 311 LLHSRLV 317
L
Sbjct: 913 RLEELEA 919
Score = 35.5 bits (82), Expect = 0.11
Identities = 49/328 (14%), Positives = 120/328 (36%), Gaps = 67/328 (20%)
Query: 187 IERNWSRLLAAHQEKDSILQDEIKRLDRLQRL----------AEKVTREMKRVDGRLEEL 236
+E L +E + + ++ + ++ L E++ E+ + +EEL
Sbjct: 241 LEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEEL 300
Query: 237 ESRINEEARRLDRLH--PLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDL 294
E I+ RL+ L + + ++ L+ + +E + + +TL E ++L
Sbjct: 301 EGEISLLRERLEELENELEELEERLEELKEKIEALKEEL----EERETLLEELEQLLAEL 356
Query: 295 HKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRA 354
+ ++L ++ + L + F A
Sbjct: 357 EEAKEELEEK------------------------------------LSALLEELEELFEA 380
Query: 355 LQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEI 414
L+E + ++ +LA+I+ +L+ ++ EI + +++ + D +L+ ++AE+
Sbjct: 381 LREELAELEAELAEIRN-----ELEELKREIESLEERLERLSE-RLEDLKEELKELEAEL 434
Query: 415 AIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRR 474
Q E +E+ + +E + K L + +L EE + +L
Sbjct: 435 EELQTE---LEELNEELEELEEQL------EELRDRLKELERELAELQEELQRLEKELSS 485
Query: 475 LRREMDEVNRLFDEFERRARAEEDMKNA 502
L +D + + E +++
Sbjct: 486 LEARLDRLEAEQRASQGVRAVLEALESG 513
Score = 29.7 bits (67), Expect = 6.6
Identities = 24/116 (20%), Positives = 50/116 (43%), Gaps = 6/116 (5%)
Query: 468 SDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASNLQSKLDEAER----- 522
S Q R L+ +E+ L + E+ + +KN + + L+ +L+E ER
Sbjct: 662 SLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEEL 721
Query: 523 -TLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQDRGEAL 577
+ + + + LE L + ++ E L+ L LE+ E + ++++ L
Sbjct: 722 KRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKL 777
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 41.8 bits (99), Expect = 0.001
Identities = 26/121 (21%), Positives = 45/121 (37%), Gaps = 12/121 (9%)
Query: 192 SRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLH 251
L E D L + + L+ E+ + E++ LE +R+ E RL L
Sbjct: 251 LEALEDLSEYDGKLSELAELLEEALYELEEASEELRAYLDELEFDPNRLEEVEERLFALK 310
Query: 252 PLDAKHNVDVLE------------HDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQ 299
L K+ V + + L +EE++ L +V+ L+ A L +
Sbjct: 311 SLARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSAIRK 370
Query: 300 K 300
K
Sbjct: 371 K 371
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily
archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and C-terminal
domains of this protein are well conserved, but the
central hinge region is skewed in composition and highly
divergent [Cellular processes, Cell division, DNA
metabolism, Chromosome-associated proteins].
Length = 1164
Score = 40.8 bits (96), Expect = 0.003
Identities = 59/342 (17%), Positives = 130/342 (38%), Gaps = 54/342 (15%)
Query: 187 IERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARR 246
IE+ +L ++ L++ + L L++ E V E+K ++ R+EELE +++
Sbjct: 721 IEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEA 780
Query: 247 LDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWV 306
L+ L + + ++ +L + EE ++ + E R ++ +++ +L
Sbjct: 781 LNDLEARLSHSRIPEIQAELSKLEEEVSRI--------EAR---LREIEQKLNRLTLEKE 829
Query: 307 ALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKL 366
L + + E+R ++ +E + + N L+E +E
Sbjct: 830 YLEKEIQE------------LQEQRIDLKEQIKSIEKEIENLNGKKEELEEELE-----E 872
Query: 367 AQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIAIHQREQNIIEQ 426
+ D S L ++ E + AQ++E + + + E I ++ + + E
Sbjct: 873 LEAALRDLESRLGDLKKER------DELEAQLRELERKIE----ELEAQIEKKRKRLSEL 922
Query: 427 FHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLR-----REMDE 481
L + + I ED + EE D Q R R ++
Sbjct: 923 KAK----------LEALEEELSEIEDPKGEDEEIPEEELSLEDVQAELQRVEEEIRALEP 972
Query: 482 VN-RLFDEFERRARAEEDMKNATKLFTEKASNLQSKLDEAER 522
VN E+E + +++K E+ + +++E E+
Sbjct: 973 VNMLAIQEYEEVLKRLDELKEKRAKLEEERKAILERIEEYEK 1014
Score = 40.1 bits (94), Expect = 0.004
Identities = 38/222 (17%), Positives = 83/222 (37%), Gaps = 44/222 (19%)
Query: 133 EMKKLAADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWS 192
E+K+L A + + D +L+ DL E + I I+ S
Sbjct: 759 ELKELEA--------RIEELEEDLHKLEEALNDL--------EARLSHS-RIPEIQAELS 801
Query: 193 RLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLD---- 248
+L ++ L++ ++L+RL E + +E++ + + +L+ +I + ++
Sbjct: 802 KLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNG 861
Query: 249 --------------RLHPLDAKH-----NVDVLEHDLRQAEENINTLFSDVQTLREGRYP 289
L L+++ D LE LR+ E I L + ++ R+
Sbjct: 862 KKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRK---- 917
Query: 290 QASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEER 331
+ S+L +++ L + + P +S V+
Sbjct: 918 RLSELKAKLEALEEELSEIEDPKGEDEEIPEEELSLEDVQAE 959
Score = 40.1 bits (94), Expect = 0.004
Identities = 74/395 (18%), Positives = 150/395 (37%), Gaps = 75/395 (18%)
Query: 207 DEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAK---------- 256
DEI + R EK E++ V+ +E L+ I+E+ ++L+RL K
Sbjct: 160 DEIAGVAEFDRKKEKALEELEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKE 219
Query: 257 ---HNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLH 313
+ L + E + + +L E + L + + +L +R + LL
Sbjct: 220 KREYEGYELLKEKEALERQKEAIERQLASLEE----ELEKLTEEISELEKRLEEIEQLL- 274
Query: 314 SRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEAD 373
+ ++ + + E ++E I ++ ++A ++ +
Sbjct: 275 -----------------EELNKKIKDLGEEEQ-------LRVKEKIGELEAEIASLERS- 309
Query: 374 YGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIAIHQREQNIIEQFHTRVEH 433
IA +RE A+ + A +++ + AEI +RE IE+ R +
Sbjct: 310 -----------IAEKERELE-DAEERLAKLEAEIDKLLAEIEELERE---IEEERKRRDK 354
Query: 434 CIAAKFLAMGAAQRNAIRKALNE---DADKLLEEGDPSDPQLRRLRREMDEVN----RLF 486
A + +R L E + + +E +L +L+RE++E+ RL
Sbjct: 355 LTEE--YAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQ 412
Query: 487 DEFERRARAEEDMKNATKLFTEKASNLQS-------KLDEAERTLHSRINAPVPRDLDSL 539
+E +R + D+ A K + L+ ++ + E L ++ A + + L
Sbjct: 413 EELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKL-EQLAADLSKYEQEL 471
Query: 540 EHLVLQHKDFESTLKNLMSDLEKREIQFSAVQDRG 574
L ++ E L L +L + E Q A ++R
Sbjct: 472 YDLKEEYDRVEKELSKLQRELAEAEAQARASEERV 506
Score = 35.8 bits (83), Expect = 0.078
Identities = 62/323 (19%), Positives = 122/323 (37%), Gaps = 38/323 (11%)
Query: 181 ELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRI 240
L + E LL + + + ++L L+ EK+T E+ ++ RLEE+E +
Sbjct: 215 ALLKEKREYEGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLL 274
Query: 241 NEEARRLDRL---HPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKR 297
E +++ L L K + LE ++ E +I +++ D +R
Sbjct: 275 EELNKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELE-----------DAEER 323
Query: 298 VQKLHQRWVALRSLLHS--RLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRAL 355
+ KL L + + R + + EE ++ + L + + F
Sbjct: 324 LAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAET 383
Query: 356 QEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIA 415
++ +L +E L+ ++ EI +RE + + +LQ + E+A
Sbjct: 384 RD-------ELKDYREK-----LEKLKREINELKRELDRL--------QEELQRLSEELA 423
Query: 416 IHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRL 475
IE +E K L + + + L D K +E + R+
Sbjct: 424 DLNAAIAGIEAKINELEEEKEDKALEIKKQEWK--LEQLAADLSKYEQELYDLKEEYDRV 481
Query: 476 RREMDEVNRLFDEFERRARAEED 498
+E+ ++ R E E +ARA E+
Sbjct: 482 EKELSKLQRELAEAEAQARASEE 504
Score = 35.4 bits (82), Expect = 0.12
Identities = 40/236 (16%), Positives = 89/236 (37%), Gaps = 31/236 (13%)
Query: 354 ALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAE 413
+LQ + ++N+L ++ + L +I ++E + Q +E ++
Sbjct: 692 SLQSELRRIENRLDELSQE-----LSDASRKIGEIEKEIEQLEQEEEK--------LKER 738
Query: 414 IAIHQREQNIIEQFHTRVEHCIA--AKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQ 471
+ + + + +EQ V+ + + + + +ALN+ +L +
Sbjct: 739 LEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHS------R 792
Query: 472 LRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKAS----NLQSKLDEAERTLHSR 527
+ ++ E+ ++ E R R E N L E LQ + + + + S
Sbjct: 793 IPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSI 852
Query: 528 ------INAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQDRGEAL 577
+N + LE L +D ES L +L + ++ E Q ++ + E L
Sbjct: 853 EKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEEL 908
Score = 33.9 bits (78), Expect = 0.30
Identities = 37/188 (19%), Positives = 78/188 (41%), Gaps = 15/188 (7%)
Query: 407 LQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRN--AIRK---ALNEDADKL 461
LQ ++ + +RE + ++ R+E+ + + A R I K L ++ +KL
Sbjct: 676 LQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKL 735
Query: 462 LEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTE--KASNLQSKLDE 519
E + + L L +E++ V E E R E+ + + +A S++ E
Sbjct: 736 KERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPE 795
Query: 520 AERTL------HSRINAPVPRDLDSLEHLVLQHKDF-ESTLKNLMSDLEKREIQFSAVQD 572
+ L SRI A + R+++ + + K++ E ++ L + Q +++
Sbjct: 796 IQAELSKLEEEVSRIEARL-REIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEK 854
Query: 573 RGEALILQ 580
E L +
Sbjct: 855 EIENLNGK 862
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 39.7 bits (93), Expect = 0.005
Identities = 73/431 (16%), Positives = 176/431 (40%), Gaps = 27/431 (6%)
Query: 153 QRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRL 212
+ ++RL+ + + L K ++ E+ + ++E L +E + L+ ++RL
Sbjct: 325 KSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERL 384
Query: 213 DRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEEN 272
+L+ +++ E+ + LEE++ + E + L+ + + ++ LE ++++ EE
Sbjct: 385 KQLEEAIQELKEELAELSAALEEIQEELEELEKELE-----ELERELEELEEEIKKLEEQ 439
Query: 273 INTLFSDVQTLREGRYPQA---------SDLHKRVQKLHQRWVALRSLLHSRLVSPLASM 323
IN L S + E + H++ + L L +
Sbjct: 440 INQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYE-LELEELEEELSREKEEAE 498
Query: 324 SFPVVEERTVTRQTRTVMETRLVDTNTHFRA-LQEAIEWVKNKLAQIQEADYGSDLQGVQ 382
+EE + L++ + L+E +E ++N L +++E LQ ++
Sbjct: 499 LREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLK 558
Query: 383 AEIA-IHQREQNIIAQIQEA----DYGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAA 437
E+ + R Q + ++E +L+ ++ + +++ +E+ +++E + +
Sbjct: 559 EELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQS 618
Query: 438 KFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEE 497
+ N + +A E+ + LE+ + L+ ++E+ +E E R E
Sbjct: 619 ---LELSEAENELEEAE-EELESELEKLNLQAELEELLQAALEELEEKVEELEAEIRREL 674
Query: 498 DMKNATKLFTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLM 557
+ EK L+ +E E+ + + L +E L+ + + ++ L+ L
Sbjct: 675 QRIENEEQLEEKLEELEQLEEELEQLREEL--EELLKKLGEIEQLIEELESRKAELEELK 732
Query: 558 SDLEKREIQFS 568
+LEK E
Sbjct: 733 KELEKLEKALE 743
Score = 35.5 bits (82), Expect = 0.10
Identities = 90/533 (16%), Positives = 198/533 (37%), Gaps = 70/533 (13%)
Query: 134 MKKLAADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSR 193
+ L + + + + L+ I L E++ E+ E+ + E +
Sbjct: 173 SELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQ 232
Query: 194 LLAAHQEKDSILQDEIKRLDRLQ-RLAEKVTREMKRVDGR---LEELESRINEEARRLDR 249
+ A +E+ + L++E +RL+ L+ RL E + E++ + R L ELE + E +++R
Sbjct: 233 EIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIER 292
Query: 250 LHPLDAKHNVDV--------LEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKL 301
L L+ + L +L + E + +L ++ L E + L +++L
Sbjct: 293 LEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEE----KLEKLESELEEL 348
Query: 302 HQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVME-------TRLVDTNTHFRA 354
+ L LL RL L + +E + +E L + +
Sbjct: 349 AEEKNELAKLLEERL-KELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEE 407
Query: 355 LQEAIEWVKNKLAQIQEA--DYGSDLQGVQAEIAIHQREQNIIAQIQEAD---------- 402
+QE +E ++ +L +++ + +++ ++ +I + ++ +IA++ A
Sbjct: 408 IQEELEELEKELEELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQEL 467
Query: 403 -----------YGSDLQGVQAEIAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIR 451
Y +L+ ++ E++ + E + E+ + + + +
Sbjct: 468 PEEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEAL 527
Query: 452 KAL----NEDADKLLEEGDPSD--PQLRRLRREMDEVNRLFDEF---ERRARAEEDMKNA 502
K E + LLEE + QL++L+ E+ ++ E R K
Sbjct: 528 KEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEE 587
Query: 503 TKLFTEKASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEK 562
+ E+ L+ KL E E L +L E + ++ E L++ + L
Sbjct: 588 LEELRERLKELKKKLKELEERLSQLEELLQSLELSEAE---NELEEAEEELESELEKLNL 644
Query: 563 REIQFSAVQDRGEALILQHHPAAKCIEAYMAAMQSQWAWLLQLALCLETHLKH 615
+ +Q E L E + ++++ LQ E +
Sbjct: 645 QAELEELLQAALEEL-----------EEKVEELEAEIRRELQRIENEEQLEEK 686
Score = 35.1 bits (81), Expect = 0.14
Identities = 53/300 (17%), Positives = 121/300 (40%), Gaps = 45/300 (15%)
Query: 195 LAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLD 254
L+ +E+ + ++ + L+ L E++ ++ + EELE ++ + L+ L L
Sbjct: 490 LSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELK 549
Query: 255 AKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQAS--DLHKRVQKLHQRWVALRSLL 312
K + L+ +LRQ E+ + L ++ LR R + +L +R+++L ++ L L
Sbjct: 550 EKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELEERL 609
Query: 313 HSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEA 372
E + + + L+EA E ++++L ++
Sbjct: 610 SQ--------------LEELLQSL----------ELSEAENELEEAEEELESELEKLNLQ 645
Query: 373 DYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIA-IHQREQNIIEQFHTRV 431
E + + + +++E ++AEI QR +N +
Sbjct: 646 AE--------LEELLQAALEELEEKVEE---------LEAEIRRELQRIENEEQLEEKLE 688
Query: 432 EHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFER 491
E + L + + K L E ++L+EE + +L L++E++++ + + E
Sbjct: 689 ELEQLEEELEQLREELEELLKKLGE-IEQLIEELESRKAELEELKKELEKLEKALELLEE 747
Score = 32.8 bits (75), Expect = 0.64
Identities = 67/340 (19%), Positives = 130/340 (38%), Gaps = 51/340 (15%)
Query: 194 LLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRI------------- 240
L + +E+ IL DE+ L++ ++L+E + +K ++EELE ++
Sbjct: 149 LKSKPKERKEIL-DELFGLEKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEA 207
Query: 241 -NEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQ 299
EE + L +L + + + LE ++ EE + L + + L E + ++
Sbjct: 208 LEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELE 267
Query: 300 KLHQRWVALRSL--LHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQE 357
L R LR L L L ER + ++ RAL E
Sbjct: 268 ALKIREEELRELERLLEELEE---------KIERLEELEREIEELEEELEG---LRALLE 315
Query: 358 AIEWVKNKLAQIQEA--DYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIA 415
+E + KL ++E L+ +++E+ E+N +A++ E E+
Sbjct: 316 ELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEE--------RLKEL- 366
Query: 416 IHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRL 475
+ +E+ +E K L AI++ E A+ + +L L
Sbjct: 367 -----EERLEELEKELE-----KALERLKQLEEAIQELKEELAELSAALEE-IQEELEEL 415
Query: 476 RREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASNLQS 515
+E++E+ R +E E + E+ N + + L
Sbjct: 416 EKELEELERELEELEEEIKKLEEQINQLESKELMIAELAG 455
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 38.5 bits (90), Expect = 0.010
Identities = 50/232 (21%), Positives = 84/232 (36%), Gaps = 45/232 (19%)
Query: 370 QEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIAIHQREQNIIEQFHT 429
Q Y L+ + + ++E I QE DY S++ Q E+ + E N
Sbjct: 169 QIKTYEKKLEAAENRLKAFKQENGGILPDQEGDYYSEISEAQEELEAARLELN------- 221
Query: 430 RVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEE----GDPSDPQLRRLRREMD----- 480
AQR+A+++ L + LL D ++ L +++D
Sbjct: 222 ------------EAIAQRDALKRQLGGEEPVLLAGSSVANSELDGRIEALEKQLDALRLR 269
Query: 481 ---------EVNRLFDEFERRARAEEDMKNATKLFTEKAS----NLQSKLDEAERTLHSR 527
R + E + E KN E A+ LQ +L EAE + S
Sbjct: 270 YTDKHPDVIATKREIAQLEEQKEEEGSAKNGGPERGEIANPVYQQLQIELAEAEAEIAS- 328
Query: 528 INAPVP---RDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQDRGEA 576
+ A V ++ LE L+ + E+ L L D E + + + R E+
Sbjct: 329 LEARVAELTARIERLESLLRTIPEVEAELTQLNRDYEVNKSNYEQLLTRRES 380
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 37.6 bits (88), Expect = 0.019
Identities = 20/108 (18%), Positives = 37/108 (34%), Gaps = 11/108 (10%)
Query: 378 LQGVQAEIAIHQREQNIIAQIQEADYGSD--LQGVQAEIAIHQREQNIIEQFHTRVEHCI 435
L+ ++ IA + E + + + D L ++AE+A + E + R +
Sbjct: 421 LEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAE---LAALEARWQQEK 477
Query: 436 AAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVN 483
A+R L DAD ++ QL L +
Sbjct: 478 EL------VEAILALRAELEADADAPADDDAALRAQLAELEAALASAQ 519
Score = 30.7 bits (70), Expect = 3.0
Identities = 27/140 (19%), Positives = 50/140 (35%), Gaps = 16/140 (11%)
Query: 184 IDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKR---VDGRLEELESRI 240
+ +++ +R+ + + L+D +R+ L+ + + RE D RL EL + +
Sbjct: 400 VSLLDTACARVALSQNATPAALEDLRRRIAALELELDALEREAALGADHDERLAELRAEL 459
Query: 241 NEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQK 300
L LE +Q +E + + + L A D +
Sbjct: 460 AALEAEL------------AALEARWQQEKELVEAILALRAELEADADAPADDDAALRAQ 507
Query: 301 LHQRWVALRSLLHS-RLVSP 319
L + AL S LV P
Sbjct: 508 LAELEAALASAQGEEPLVFP 527
>gnl|CDD|215960 pfam00509, Hemagglutinin, Haemagglutinin. Hemagglutinin from
influenza virus causes membrane fusion of the viral
membrane with the host membrane. Fusion occurs after the
host cell internalises the virus by endocytosis. The
drop of pH causes release of a hydrophobic fusion
peptide and a large conformational change leading to
membrane fusion.
Length = 550
Score = 36.2 bits (84), Expect = 0.052
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 16/83 (19%)
Query: 214 RLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAK-----HNVDVL-----E 263
+L L EK+ + + ++ ELE RIN +++D D +N ++L +
Sbjct: 379 KLNSLIEKMNTQFEAIEKEFSELERRINNLNKKVD-----DGITDIWSYNAELLVLLENQ 433
Query: 264 HDLRQAEENINTLFSDVQT-LRE 285
H L + N+N L+ V+ LRE
Sbjct: 434 HTLDLHDSNVNNLYEKVRRQLRE 456
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 35.8 bits (83), Expect = 0.069
Identities = 18/83 (21%), Positives = 41/83 (49%)
Query: 166 LTKYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTRE 225
Y++D +D+ P +E+ ++ L E+D I Q + +L++ +K+ +
Sbjct: 242 PNYYYKDEKYLDVVPLKAYADLEKLFNEALDEKFERDKIKQLASELEKKLEKELKKLENK 301
Query: 226 MKRVDGRLEELESRINEEARRLD 248
+++ + LEELE E ++ +
Sbjct: 302 LEKQEDELEELEKAAEELRQKGE 324
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 34.5 bits (80), Expect = 0.20
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 229 VDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLRE--- 285
V L ++E + E D+ L AK + +E L EE+I + ++ L+E
Sbjct: 73 VTNSLPDIEELLFEAEELNDKFRFLKAKKAIKEIEELLDTIEEDIEQILEELNELKESEE 132
Query: 286 ---GRYPQASDLHKRVQK 300
+ D ++ ++K
Sbjct: 133 KNRKEVEELKDKYRELRK 150
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 34.3 bits (79), Expect = 0.26
Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 13/105 (12%)
Query: 189 RNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRIN------- 241
+ L A +E L+ E K L +L+ +K E+ + RLEEL +
Sbjct: 602 NEYLELKDAEKE----LEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYS 657
Query: 242 -EEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLRE 285
EE L + L+ + L +L + E+ + ++ L+E
Sbjct: 658 EEEYEELREEY-LELSRELAGLRAELEELEKRREEIKKTLEKLKE 701
Score = 33.1 bits (76), Expect = 0.57
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 451 RKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLF--TE 508
K L E+ DK EE ++ +L LR+E++E+ + + E E EE ++ + +L
Sbjct: 621 LKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRA 680
Query: 509 KASNLQSKLDEAERTL 524
+ L+ + +E ++TL
Sbjct: 681 ELEELEKRREEIKKTL 696
Score = 30.0 bits (68), Expect = 5.4
Identities = 21/106 (19%), Positives = 44/106 (41%), Gaps = 23/106 (21%)
Query: 203 SILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEA--------RRLDRLHPL- 253
L+ E+++L+ L++ ++ +++ ++ L EL + E RL L P
Sbjct: 542 KSLKKELEKLEELKKKLAELEKKLDELEEELAELLKELEELGFESVEELEERLKELEPFY 601
Query: 254 -------DAKHNV-------DVLEHDLRQAEENINTLFSDVQTLRE 285
DA+ + LE +L +A E + ++ LR+
Sbjct: 602 NEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRK 647
>gnl|CDD|233420 TIGR01452, PGP_euk, phosphoglycolate/pyridoxal phosphate
phosphatase family. PGP is an essential enzyme in the
glycolate salvage pathway in higher organisms
(photorespiration in plants). Phosphoglycolate results
from the oxidase activity of RubisCO in the Calvin cycle
when concentrations of carbon dioxide are low relative
to oxygen. In mammals, PGP is found in many tissues,
notably in red blood cells where P-glycolate is and
important activator of the hydrolysis of
2,3-bisphosphoglycerate, a major modifier of the oxygen
affinity of hemoglobin. Pyridoxal phosphate (PLP,
Vitamin B6) phosphatase is involved in the degradation
of PLP in mammals and is widely distributed in human
tissues including erythrocyes. The enzymes described
here are members of the Haloacid dehalogenase
superfamily of hydrolase enzymes (pfam00702). Unlike the
bacterial PGP equivalog (TIGR01449), which is a member
of class (subfamily) I, these enzymes are members of
class (subfamily) II. These two families have almost
certainly arisen from convergent evolution (although
these two ancestors may themselves have diverged from a
more distant HAD superfamily progenitor). The primary
seed sequence for this model comes from Chlamydomonas
reinhardtii, a photosynthetic alga. The enzyme has been
purified and characterized and these data are fully
consistent with the assignment of function as a PGPase
involved in photorespiration. The second seed, from Homo
sapiens chromosome 22 has been characterized as a
pyridoxal phosphatase. Biochemical characterization of
partially purified PGP's from various tissues including
red blood cells have been performed while one gene for
PGP has been localized to chromosome 16p13.3. The
sequence used here maps to chromosome 22. There is
indeed a related gene on chromosome 16 (and it is
expressed, since EST's are found) which shows 46%
identity and 59% positives by BLAST2 (E=1e-66). The
chromosome 16 gene is not in evidence in nraa but
translated from the genomic sequence would score 372.4
(E=7.9e-113) versus This model, well above trusted. The
third seed, from C. elegans, is only supported by
sequence similarity. This model is limited to eukaryotic
species including S. pombe and S. cerevisiae, although
several archaea score between the trusted and noise
cutoffs. This model is closely related to a family of
bacterial sequences including the E. coli NagD and B.
subtilus AraL genes which are characterized by the
ability to hydrolyze para-nitrophenylphosphate (pNPPases
or NPPases). The chlamydomonas PGPase d.
Length = 279
Score = 33.3 bits (76), Expect = 0.30
Identities = 21/78 (26%), Positives = 29/78 (37%), Gaps = 3/78 (3%)
Query: 457 DADKLLEEGD---PSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASNL 513
D D +L G+ P P+L + ++RAE +K A F A L
Sbjct: 8 DCDGVLWLGERVVPGAPELLDRLARAGKAALFVTNNSTKSRAEYALKFARLGFNGLAEQL 67
Query: 514 QSKLDEAERTLHSRINAP 531
S A R L +AP
Sbjct: 68 FSSALCAARLLRQPPDAP 85
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 33.0 bits (76), Expect = 0.63
Identities = 63/315 (20%), Positives = 121/315 (38%), Gaps = 38/315 (12%)
Query: 192 SRLLAAHQEKDSILQDEIKRL-DRLQRL--AEKVTREMKRVDGRLEELESRINEEARRLD 248
+R LA E +S L+ + + D L + A + +++R LEELE R+ E+ ++
Sbjct: 313 ARELAELNEAESDLEQDYQAASDHLNLVQTALRQQEKIERYQADLEELEERLEEQNEVVE 372
Query: 249 RLHPLDAKHNVDVLEHDLRQAEENINTLFS---------DVQTLREGRYPQASDLHKRVQ 299
+A + E AEE ++ L S DVQ R +Y QA +R +
Sbjct: 373 -----EADEQQEENEARAEAAEEEVDELKSQLADYQQALDVQQTRAIQYQQAVQALERAK 427
Query: 300 KLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAI 359
+ L L L +E+ T + +E +L ++A
Sbjct: 428 Q----LCGLPDLTADNAEDWLEEF---QAKEQEAT-EELLSLEQKLSVAQAAHSQFEQAY 479
Query: 360 EWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQAEIAIHQR 419
+ V+ ++ S+ V E+ REQ +A+ Q L ++ + QR
Sbjct: 480 QLVRKIAGEVSR----SEAWDVARELLRRLREQRHLAE-QLQQLRMRLSELEQRLRQQQR 534
Query: 420 EQNIIEQFHTRVE-HCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRRE 478
+ ++ +F R+ + L + A ++L+E + E + LR++
Sbjct: 535 AERLLAEFCKRLGKNLDDEDELEQLQEELEARLESLSESVSEARE-------RRMALRQQ 587
Query: 479 MDEVNRLFDEFERRA 493
++++ RA
Sbjct: 588 LEQLQARIQRLAARA 602
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 32.9 bits (75), Expect = 0.66
Identities = 30/122 (24%), Positives = 48/122 (39%), Gaps = 15/122 (12%)
Query: 424 IEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVN 483
IE+ ++ +AMG +R L E+ K + P L M+++
Sbjct: 464 IEKLKKEIDLEYTEAVIAMGLQERLE---NLREEFSKANSQDQLMHPVL------MEKIE 514
Query: 484 RLFDEFER---RARAEEDMKNATKLFTE--KASNLQSKLDEAERTLHSRINAPVPRDLDS 538
+L DEF + RA +K + E +A L K +AE L + IN +D
Sbjct: 515 KLKDEFNKRLSRAPNYLSLKYKLDMLNEFSRAKALSEKKSKAE-KLKAEINKKFKEVMDR 573
Query: 539 LE 540
E
Sbjct: 574 PE 575
>gnl|CDD|215018 smart01087, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 598
Score = 32.7 bits (75), Expect = 0.72
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 447 RNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLF 506
R+ + K L + + L E P QL+RL ++ ++N D + + KN T+
Sbjct: 9 RSDLEKRLLKINGEFLSEFKPVAEQLQRLSEDVQKLNNSCDSMKDQLNTA---KNQTQDL 65
Query: 507 TEKASNLQSKLDEAE 521
+AS LQ +L E
Sbjct: 66 ISEASELQEELALLE 80
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 32.4 bits (74), Expect = 0.78
Identities = 54/295 (18%), Positives = 100/295 (33%), Gaps = 61/295 (20%)
Query: 205 LQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRL-HPL-DAKHNVDVL 262
+ K+L ++Q+ + ++++ + +LE ++ + L L + ++ L
Sbjct: 33 AAADDKQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKL 92
Query: 263 EHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWV---ALRSLLHSRLVSP 319
+ +N L VQ+ QR L +L S P
Sbjct: 93 RKQIADLNARLNAL--------------------EVQEREQRRRLAEQLAALQRSGRNPP 132
Query: 320 LASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQ 379
A + P +R+V RL ++ AL A + L + L
Sbjct: 133 PALLVSPEDAQRSV----------RLA---IYYGALNPARAERIDALKATLK-----QLA 174
Query: 380 GVQAEIAIHQRE-----------QNIIAQIQ------EADYGSDLQGVQAEIAIHQREQN 422
V+AEIA Q E Q +AQ+ A S+L Q ++ + ++
Sbjct: 175 AVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELRANES 234
Query: 423 IIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRR 477
++ E A A AA A +A +A + E P+ P+ +
Sbjct: 235 RLKNEIASAEAAAAKAREAA-AAAEAAAARARAAEAKRTGETYKPTAPEKMLISS 288
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 32.1 bits (74), Expect = 1.0
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 229 VDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLRE--- 285
V L ++E ++ E D+ AKH ++ +E L EE+I + ++Q L E
Sbjct: 77 VTNSLPDIEEQLFEAEELNDKFRFRKAKHEINEIESLLDLIEEDIEQILEELQELLESEE 136
Query: 286 ---GRYPQASDLHKRVQK 300
Q DL++ ++K
Sbjct: 137 KNREEVEQLKDLYRELRK 154
>gnl|CDD|237259 PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed.
Length = 830
Score = 32.0 bits (74), Expect = 1.1
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 465 GDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASN---LQSKLDEA 520
G +D +L+RLR+ +D++N L E E ++E++K T F E+ + L L EA
Sbjct: 10 GSRNDRELKRLRKIVDKINALEPEME--KLSDEELKAKTAEFKERLAKGETLDDLLPEA 66
>gnl|CDD|233228 TIGR00998, 8a0101, efflux pump membrane protein (multidrug
resistance protein A). [Transport and binding proteins,
Other].
Length = 334
Score = 31.7 bits (72), Expect = 1.1
Identities = 35/179 (19%), Positives = 59/179 (32%), Gaps = 21/179 (11%)
Query: 226 MKRVDGRLEELESRINEEARRLD---RLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQT 282
+V G + E+ + ++ D RL P +A+ + E +L L VQ
Sbjct: 46 SSQVSGSVIEVNVDDTDYVKQGDVLVRLDPTNAELALAKAEANLAALVRQTKQLEITVQQ 105
Query: 283 L--------------REGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVV 328
L RE DL +RV + ++ L H+R A +
Sbjct: 106 LQAKVESLKIKLEQAREKLLQAELDLRRRVPLFKKGLISREELDHARKALLSAKAALNAA 165
Query: 329 EERTVTRQTRTVMETRLVDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAI 387
+ + V T L A+QEA E +K ++ + G A +
Sbjct: 166 IQEQLNANQALVRGTPLKKQ----PAVQEAKERLKTAWLALKRTVIRAPFDGYVARRFV 220
>gnl|CDD|236530 PRK09466, metL, bifunctional aspartate kinase II/homoserine
dehydrogenase II; Provisional.
Length = 810
Score = 31.8 bits (73), Expect = 1.2
Identities = 28/129 (21%), Positives = 49/129 (37%), Gaps = 29/129 (22%)
Query: 521 ERTLHSRINAPVPRDLDS---LEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQDRGEAL 577
ER L S A + LD +E V DF+ K L L++ ++ L
Sbjct: 299 ERVLASGTGARIVTSLDDVCLIELQVPASHDFKLAQKELDQLLKRAQL---------RPL 349
Query: 578 ILQHHPAAKCIE-AYMAAMQSQ-WAWLLQLALCLETHLK---------------HAAYYH 620
+ HP + ++ AY + + L AL E L+ + + H
Sbjct: 350 AVGVHPDRQLLQLAYTSEVADSALKLLDDAALPGELKLREGLALVALVGAGVTRNPLHCH 409
Query: 621 QFWREMKDA 629
+F++++KD
Sbjct: 410 RFYQQLKDQ 418
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 31.9 bits (72), Expect = 1.3
Identities = 32/149 (21%), Positives = 62/149 (41%), Gaps = 20/149 (13%)
Query: 131 LIEMKKLAADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERN 190
L++ K + + + P + + ++ + ++ EV +PE + +
Sbjct: 76 LLKQKSYTEPERKKTLQTLKPLSERLEEKESAIYEIESF--ELEEVITEPERPVGL---- 129
Query: 191 WSRLLAAHQEKDSILQDEI-----KRLDRLQRLAEKVTREMKRVDGRLEELESRINEEAR 245
EK+S L+ E ++ LQRL E++ RE +EE+ S++ E
Sbjct: 130 --SFEKELFEKNSFLESETTIVRKEKDSPLQRLGERLVRE-GMSQSYVEEMASKLEE--- 183
Query: 246 RLDRLHPLDAKHNVDVLEHDLRQAEENIN 274
RL P+D N +V E + EE ++
Sbjct: 184 ---RLSPVDQGRNHNVTERAVTYLEERVS 209
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 31.2 bits (71), Expect = 1.4
Identities = 20/87 (22%), Positives = 30/87 (34%), Gaps = 14/87 (16%)
Query: 436 AAKFLAMGAAQRNAIRKALNED-ADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRAR 494
AK + K E+ + LEE P D +LR R+ +
Sbjct: 57 KAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRL-------------RKLQ 103
Query: 495 AEEDMKNATKLFTEKASNLQSKLDEAE 521
E D+ NA LF A + L+ +
Sbjct: 104 EESDLNNAADLFGGPAPTKDTDLESLD 130
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 31.6 bits (72), Expect = 1.4
Identities = 20/115 (17%), Positives = 47/115 (40%), Gaps = 23/115 (20%)
Query: 469 DPQLRRLRREMDEVNRL--------FDEFERRARAEEDMKNATKLFTEKASNLQSKLDEA 520
D R+LR+ ++ +L ++ D++ E+ +L++++ E
Sbjct: 34 DEVERKLRKLESKIKKLGIPLKDTGGKPDVPPSKEFLDLE-------EEILDLEAEIKEV 86
Query: 521 E---RTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQD 572
E +L IN +L+ +++ + K F +S+L +I F ++
Sbjct: 87 EENLESLEKEIN-----ELEEWLNVLDEEKSFLDENLEELSELSNLDIDFKYLRG 136
>gnl|CDD|227559 COG5234, CIN1, Beta-tubulin folding cofactor D [Posttranslational
modification, protein turnover, chaperones /
Cytoskeleton].
Length = 993
Score = 31.8 bits (72), Expect = 1.5
Identities = 21/120 (17%), Positives = 44/120 (36%), Gaps = 15/120 (12%)
Query: 154 RDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRL- 212
D R+ F + +G +D+ E ID++ +S LL K + + ++ L
Sbjct: 559 ADDIRVFRAFFSE-AFSVIIGAIDLQEETIIDIVSDAYSVLL-----KFDDMPETLEVLL 612
Query: 213 DRLQRLAEKVTREMKRVDGRLEE---LESRINEEARRL-----DRLHPLDAKHNVDVLEH 264
D + + + + + + R E+ +L +LH +D + H
Sbjct: 613 DYIVKCSTSKEARIVYSILQNTPSLIISFRYQEKICKLLLDIYPQLHSIDYSAPIANALH 672
>gnl|CDD|147523 pfam05384, DegS, Sensor protein DegS. This is small family of
Bacillus DegS proteins. The DegS-DegU two-component
regulatory system of Bacillus subtilis controls various
processes that characterize the transition from the
exponential to the stationary growth phase, including
the induction of extracellular degradative enzymes,
expression of late competence genes and down-regulation
of the sigma D regulon. The family also contains one
sequence from Thermoanaerobacter tengcongensis which is
described as a sensory transduction histidine kinase.
Length = 159
Score = 30.3 bits (69), Expect = 1.6
Identities = 33/130 (25%), Positives = 58/130 (44%), Gaps = 35/130 (26%)
Query: 451 RKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKA 510
+ + E+ ++++E D + Q RR R+ + EV+R FD++ +EED++ A EKA
Sbjct: 36 LEEVKEEVSEVIKEVDKLEKQERRARKRLAEVSRNFDKY-----SEEDIREA----YEKA 86
Query: 511 SNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAV 570
+LQ KL +L+ + E L+ +LE+R
Sbjct: 87 HDLQVKL------------------------ALLRQE--EKQLRKRRDELERRLKNLKET 120
Query: 571 QDRGEALILQ 580
+R E L+ Q
Sbjct: 121 IERAENLVSQ 130
>gnl|CDD|204553 pfam10779, XhlA, Haemolysin XhlA. XhlA is a cell-surface
associated haemolysin that lyses the two most prevalent
types of insect immune cells (granulocytes and
plasmatocytes) as well as rabbit and horse erythrocytes.
This family has had DUF1267, pfam06895, merged into it.
Length = 71
Score = 28.8 bits (65), Expect = 1.6
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 226 MKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDV--LEHDLRQAEENI 273
++ ++ RL +E+++ E + L DA + D+ L L + E+N
Sbjct: 1 IQDIEERLNRIETKLKEIEEDIRNLEKRDAANEKDIKNLNKRLEKIEDNT 50
>gnl|CDD|216249 pfam01025, GrpE, GrpE.
Length = 165
Score = 30.3 bits (69), Expect = 1.7
Identities = 35/116 (30%), Positives = 50/116 (43%), Gaps = 19/116 (16%)
Query: 452 KALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEK-A 510
+AL E+ ++L EE + +L RL E + R R E + + A K EK A
Sbjct: 14 EALEEELEELEEEIEELKDRLLRLLAEFENY---------RKRTEREREEAKKYAIEKFA 64
Query: 511 SNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQ 566
+L LD ER L A D+ SL + E LK L+ LEK ++
Sbjct: 65 KDLLPVLDNLERALA---AAKENEDVKSL------VEGVEMILKQLLKVLEKHGVE 111
>gnl|CDD|226883 COG4477, EzrA, Negative regulator of septation ring formation [Cell
division and chromosome partitioning].
Length = 570
Score = 31.2 bits (71), Expect = 1.8
Identities = 68/412 (16%), Positives = 147/412 (35%), Gaps = 66/412 (16%)
Query: 189 RNWSRLLAAHQEKDSILQ----DEIKRLDRLQRLAEKVT--REMKR-----VDGRLEELE 237
+N+ R+ + K+ +L DEI ++ +L + T E ++ V ++E
Sbjct: 25 KNYQRIDKLEERKNELLNLPVNDEISKVKKLHLTGQTETKFEEWRQKWDDIVTNSFADVE 84
Query: 238 SRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKR 297
+ E D+ AKH +D +E L EE+I + D+ L E +
Sbjct: 85 EHLFEAEALADKFRFNKAKHEIDDIEQQLTLIEEDIEQILEDLNELVE----SEEKNSEE 140
Query: 298 VQKLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRLVDTNTHFRALQE 357
+ + + + LR + + + P +E++ + L + + A +E
Sbjct: 141 IDHVLELYEELRRDVLAN--RHQYGEAAPELEKKLENIEEELSQFVELTSSGDYIEA-RE 197
Query: 358 AIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGSDLQGVQ----AE 413
+E + + ++ + + AE+ + + Q+Q+ G +
Sbjct: 198 VLEEAEEHMIALRS--IMERIPSLLAEL-----QTELPGQLQDLKAGYRDMKEEGYHLEH 250
Query: 414 IAIHQREQNIIEQFHTRVEHCIAAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLR 473
+ I R + + EQ + L+E ++L
Sbjct: 251 VNIDSRLERLKEQLV---------------ENSELLTQLELDEAEEELGL---------- 285
Query: 474 RLRREMDEVNRLFDEFERRARAEEDMKN-----ATKLFTEKASNLQSKLDEAERTLHSRI 528
+++ L+D ER A+ ++ L K +N K + R+
Sbjct: 286 ----IQEKIESLYDLLEREVEAKNVVEENLPILPDYLEKAKENNEHLKEEIERVKESYRL 341
Query: 529 NAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQFSAVQDRGEALILQ 580
+L S+ + K+ ES L ++ ++E +E+ +S +QD E +
Sbjct: 342 AE---TELGSVRKFEKELKELESVLDEILENIEAQEVAYSELQDNLEEIEKA 390
>gnl|CDD|130870 TIGR01811, sdhA_Bsu, succinate dehydrogenase or fumarate reductase,
flavoprotein subunit, Bacillus subtilis subgroup. This
model represents the succinate dehydrogenase
flavoprotein subunit as found in the low-GC
Gram-positive bacteria and a few other lineages. This
enzyme may act in a complete or partial TCA cycle, or
act in the opposite direction as fumarate reductase. In
some but not all species, succinate dehydrogenase and
fumarate reductase may be encoded as separate isozymes
[Energy metabolism, TCA cycle].
Length = 603
Score = 31.4 bits (71), Expect = 1.8
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 228 RVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDL 266
+ E ++ + EE R DRL + N L +L
Sbjct: 434 DMPEDAPEFQAALAEEQERFDRLLKMRGDENPYYLHREL 472
>gnl|CDD|239107 cd02429, PTH2_like, Peptidyl-tRNA hydrolase, type 2 (PTH2)_like .
Peptidyl-tRNA hydrolase activity releases tRNA from the
premature translation termination product peptidyl-tRNA.
Two structurally different enzymes have been reported
to encode such activity, Pth present in bacteria and
eukaryotes and Pth2 present in archaea and eukaryotes.
There is no functional information for this
eukaryote-specific subgroup.
Length = 116
Score = 29.7 bits (67), Expect = 1.8
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 533 PRDLDSLEHLVLQHKDFESTLKNLMSDLEKREI 565
+LD++ +VL+ D E+ LKNL S L + I
Sbjct: 49 LSNLDNMHKVVLEVPD-EAALKNLSSKLTENSI 80
>gnl|CDD|178769 PLN03230, PLN03230, acetyl-coenzyme A carboxylase carboxyl
transferase; Provisional.
Length = 431
Score = 31.1 bits (70), Expect = 1.8
Identities = 27/105 (25%), Positives = 44/105 (41%), Gaps = 7/105 (6%)
Query: 207 DEIKRLDRLQRLAEK---VTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLE 263
+K L+R + L K VT ++ + +LE+RI +E R L +D + LE
Sbjct: 56 GALKILNRFKPLKNKPKPVTLPFEK---PIVDLENRI-DEVRELANKTGVDFSAQIAELE 111
Query: 264 HDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVAL 308
Q + + + VQ L R+P V + +WV L
Sbjct: 112 ERYDQVRRELYSRLTPVQRLSVARHPNRPTFLDHVLNMTDKWVEL 156
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 29.5 bits (67), Expect = 2.0
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 179 DPELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMK 227
DPE+ ++ I ++ S L K SI + + RLQR A K ++
Sbjct: 35 DPEI-LEFILKHLSTLKFTEAVKVSIKKQKKINPKRLQRQAAKEVKKPG 82
>gnl|CDD|214937 smart00957, SecA_DEAD, SecA DEAD-like domain. SecA protein binds
to the plasma membrane where it interacts with proOmpA
to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This domain represents the N-terminal
ATP-dependent helicase domain, which is related to the.
Length = 380
Score = 30.9 bits (71), Expect = 2.1
Identities = 19/55 (34%), Positives = 35/55 (63%), Gaps = 3/55 (5%)
Query: 465 GDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASNLQSKLDE 519
G +D +L+RLR+ +D++N L E E A ++E+++ T F E+ + +S LD+
Sbjct: 6 GSKNDRELKRLRKIVDQINALEPEME--ALSDEELRAKTAEFKERLAEGES-LDD 57
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 30.8 bits (70), Expect = 2.2
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 189 RNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLD 248
R L + + L+ E++R R R + RE++ D R+E LE + E+ +R++
Sbjct: 439 SELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVE 498
Query: 249 RL 250
L
Sbjct: 499 EL 500
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit;
Provisional.
Length = 1545
Score = 31.0 bits (70), Expect = 2.2
Identities = 23/114 (20%), Positives = 37/114 (32%), Gaps = 2/114 (1%)
Query: 79 LYDVFPEPPAVHPLYDSESQQRVNEYCDLASSLHLWMREKTAYMQDRNFPSTLIEMKKLA 138
L D+ P PP + PL D + + + AY + ++ + L
Sbjct: 1397 LRDLLPVPPRLVPLTDDTGHPDLIALARKIYLYTILLGGAKAY-NENEVDRHILRGENLE 1455
Query: 139 ADSARFRTEEVPPRQRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWS 192
+ E PP+ K L+ F+ L K + E P H W
Sbjct: 1456 TQTGTEVLGE-PPKHATKAELKEFFRRLQKALVALEEASDAPSTHCAGCRDYWE 1508
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.9 bits (71), Expect = 2.6
Identities = 22/108 (20%), Positives = 52/108 (48%), Gaps = 14/108 (12%)
Query: 192 SRLLAAHQEKDSILQD------EIKRL------DRLQRLAEKVTREMKRVDGRLEELESR 239
+++ A +E IL++ IK+ + + +L + +E++ L++LE R
Sbjct: 31 AKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKR 90
Query: 240 INEEARRLDR-LHPLDAK-HNVDVLEHDLRQAEENINTLFSDVQTLRE 285
+ ++ LDR L L+ + ++ E +L Q ++ + +++ L E
Sbjct: 91 LLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIE 138
Score = 29.0 bits (66), Expect = 8.0
Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 181 ELHIDVIERN--WSRLLAAHQEKDSILQDEIKRLDR----LQRLAEKVTREMKRVDGRLE 234
E ++ ER +L +K+ L +++ L++ L++ +++ ++ + ++ + E
Sbjct: 72 EFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEE 131
Query: 235 ELESRINEEARRLDRL 250
ELE I E+ + L+R+
Sbjct: 132 ELEELIEEQLQELERI 147
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 30.9 bits (70), Expect = 2.9
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 10/83 (12%)
Query: 210 KRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQA 269
+ +D ++R E+V R V +EE+ + E+ +R D + + + + L
Sbjct: 452 RYIDLIERALEEVERHRGEVREIIEEVMKFLREQLKREDVVEKIL-----ESEDLVLVAR 506
Query: 270 EENINTLFSDVQTLREGRYPQAS 292
+ D +T Y QAS
Sbjct: 507 GGIPYLVVPDART-----YIQAS 524
>gnl|CDD|144881 pfam01452, Rota_NSP4, Rotavirus non structural protein. This
protein has been called NSP4, NSP5, NS28, and NCVP5. The
final steps in the assembly of rotavirus occur in the
lumen of the endoplasmic reticulum (ER). Targeting of
the immature inner capsid particle (ICP) to this
compartment is mediated by the cytoplasmic tail of NSP4,
located in the ER membrane.
Length = 174
Score = 29.5 bits (66), Expect = 3.1
Identities = 12/71 (16%), Positives = 34/71 (47%)
Query: 206 QDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHD 265
+ E+ D +++ A ++ +E++ +E+L +R E+ L R++ + + + ++
Sbjct: 86 KTEVTSKDEIEKQASRIVKEIREQLKMIEKLTTREIEQVELLKRIYDMLKVTSDNEIDMS 145
Query: 266 LRQAEENINTL 276
+ TL
Sbjct: 146 KETNRKAYKTL 156
>gnl|CDD|213354 cd11744, MIT_CorA-like, metal ion transporter CorA-like divalent
cation transporter superfamily. This superfamily of
essential membrane proteins is involved in transporting
divalent cations (uptake or efflux) across membranes.
They are found in most bacteria and archaea, and in some
eukaryotes. It is a functionally diverse group which
includes the Mg2+ transporters of Escherichia coli and
Salmonella typhimurium CorAs (which can also transport
Co2+, and Ni2+ ), the CorA Co2+ transporter from the
hyperthermophilic Thermotoga maritima, and the Zn2+
transporter Salmonella typhimurium ZntB, which mediates
the efflux of Zn2+ (and Cd2+). It includes five
Saccharomyces cerevisiae members: i) two plasma membrane
proteins, the Mg2+ transporter Alr1p/Swc3p and the
putative Mg2+ transporter, Alr2p, ii) two mitochondrial
inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and
Mrs2p, and iii) and the vacuole membrane protein Mnr2p,
a putative Mg2+ transporter. It also includes a family
of Arabidopsis thaliana members (AtMGTs), some of which
are localized to distinct tissues, and not all of which
can transport Mg2+. Thermotoga maritima CorA and Vibrio
parahaemolyticus and Salmonella typhimurium ZntB form
funnel-shaped homopentamers, the tip of the funnel is
formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, Mrs2p,
and Alr1p. Natural variants such as GVN and GIN, as in
some ZntB family proteins, may be associated with the
transport of different divalent cations, such as zinc
and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 286
Score = 29.9 bits (67), Expect = 3.7
Identities = 13/92 (14%), Positives = 30/92 (32%), Gaps = 4/92 (4%)
Query: 212 LDRLQRLAEKVTREMKRVDGRLEELESRINE--EARRLDRLHPLDAKHNVDVLEHDLRQA 269
++ L K+ ++ ++ L EL+ E L + + + +R
Sbjct: 108 NQLIEGLNGKIDLYLETIEETLNELDVNDEEGHYDESTYNHIAL--QKALISIRRFIRPQ 165
Query: 270 EENINTLFSDVQTLREGRYPQASDLHKRVQKL 301
+ + L L R Q H + ++
Sbjct: 166 QYALRDLIRSESELVTSRPHQYRFAHNNITRI 197
>gnl|CDD|218452 pfam05130, FlgN, FlgN protein. This family includes the FlgN
protein and export chaperone involved in flagellar
synthesis.
Length = 140
Score = 28.9 bits (65), Expect = 4.2
Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 12/109 (11%)
Query: 203 SILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVL 262
+L++E++ L+ L L E+ +K D +E LE E+ L +L + L
Sbjct: 4 ELLEEELELLEELLELLEEEQEALKAGD--IEALEELTEEKQELLAQL---------EQL 52
Query: 263 EHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSL 311
E + +Q + L L E + +L + Q+L + L+ L
Sbjct: 53 EEERQQLLAELG-LSPGPAGLSELLAAEDEELRELWQELKELLEELQEL 100
>gnl|CDD|223895 COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid
metabolism].
Length = 317
Score = 29.9 bits (68), Expect = 4.3
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 179 DPELHIDVIERNWSRLLAAHQEKDSILQDEIKRL-DRLQRLAEKVTREMKRVDGRLEELE 237
D E I +E L A +E D L DEI+RL RL L +K+ +
Sbjct: 6 DFEKPIAELEAKIDELKALAEENDVDLSDEIERLEKRLAELTKKIYSNLTP--------- 56
Query: 238 SRINEEARRLDRLHPLD 254
+ + AR DR + LD
Sbjct: 57 WQRVQLARHPDRPYTLD 73
>gnl|CDD|233065 TIGR00634, recN, DNA repair protein RecN. All proteins in this
family for which functions are known are ATP binding
proteins involved in the initiation of recombination and
recombinational repair [DNA metabolism, DNA replication,
recombination, and repair].
Length = 563
Score = 29.7 bits (67), Expect = 4.9
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 16/119 (13%)
Query: 202 DSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNV-- 259
D L++ +++ E+ TRE++ LE R+NE RL ++ L K+
Sbjct: 265 DGSLRELAEQVGNALTEVEEATRELQNYLDELEFDPERLNEIEERLAQIKRLKRKYGASV 324
Query: 260 -DVLEH---------DLRQAEENINTLFSDVQTLREGRYPQASDL----HKRVQKLHQR 304
+VLE+ L ++E++ L +V L E A L K ++L +R
Sbjct: 325 EEVLEYAEKIKEELDQLDDSDESLEALEEEVDKLEEELDKAAVALSLIRRKAAERLAKR 383
>gnl|CDD|217135 pfam02601, Exonuc_VII_L, Exonuclease VII, large subunit. This
family consist of exonuclease VII, large subunit
EC:3.1.11.6 This enzyme catalyzes exonucleolytic
cleavage in either 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. This exonuclease VII enzyme
is composed of one large subunit and 4 small ones.
Length = 295
Score = 29.6 bits (67), Expect = 5.0
Identities = 24/110 (21%), Positives = 45/110 (40%), Gaps = 5/110 (4%)
Query: 212 LDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQAEE 271
L +L+ L ++++R +K RLE+ + R+N RL L + + + L +
Sbjct: 149 LQKLEGLEQRLSRALKN---RLEKEQDRLNLLRERLKSLSRRLLEQHEERLAELRDRLIS 205
Query: 272 NINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLA 321
+I L S Q+ E + + L + L + +SPL
Sbjct: 206 SIQNLLSRKQSRLERLILNRELEKNSLLENKLATANLTAQL--KALSPLK 253
>gnl|CDD|223022 PHA03248, PHA03248, DNA packaging tegument protein UL25;
Provisional.
Length = 583
Score = 30.0 bits (68), Expect = 5.1
Identities = 19/63 (30%), Positives = 30/63 (47%)
Query: 436 AAKFLAMGAAQRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARA 495
AA LA+ A+ A AL+ A + D +LR + R+++EV + E A A
Sbjct: 51 AAARLALLEARNRAAAAALDNLAGQAATIPVEVDRRLRPIERQLEEVADALADLEEAAAA 110
Query: 496 EED 498
E+
Sbjct: 111 AEE 113
>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
Length = 438
Score = 29.8 bits (68), Expect = 5.3
Identities = 28/110 (25%), Positives = 47/110 (42%), Gaps = 5/110 (4%)
Query: 211 RLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLD----AKHNVDVLEHDL 266
R + LQRL + R + + RLE+ R+++ ARRL P + +D L+ L
Sbjct: 262 RAELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRL 321
Query: 267 RQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRL 316
++A E L R Q + +R+++ QR L L +
Sbjct: 322 QRALERRLRLAKQRLERLSQRLQQQN-PQRRIERAQQRLEQLEQRLRRAM 370
>gnl|CDD|217705 pfam03739, YjgP_YjgQ, Predicted permease YjgP/YjgQ family. Members
of this family are predicted integral membrane proteins
of unknown function. They are about 350 amino acids long
and contain about 6 transmembrane regions. They are
predicted to be permeases although there is no
verification of this.
Length = 354
Score = 29.6 bits (67), Expect = 5.3
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 258 NVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRLV 317
+ D E DL +++++L D + L + KR++ R+ LH RL
Sbjct: 221 SFDRYEIDLSLTPQDLSSLTEDPEELS---LSELYAYIKRLKASGLDVRKYRAELHRRLA 277
Query: 318 SPLASMSFPVV 328
PL+ + ++
Sbjct: 278 LPLSCLVLALL 288
>gnl|CDD|216560 pfam01544, CorA, CorA-like Mg2+ transporter protein. The CorA
transport system is the primary Mg2+ influx system of
Salmonella typhimurium and Escherichia coli. CorA is
virtually ubiquitous in the Bacteria and Archaea. There
are also eukaryotic relatives of this protein. The
family includes the MRS2 protein from yeast that is
thought to be an RNA splicing protein. However its
membership of this family suggests that its effect on
splicing is due to altered magnesium levels in the cell.
Length = 291
Score = 29.6 bits (67), Expect = 5.3
Identities = 31/161 (19%), Positives = 60/161 (37%), Gaps = 23/161 (14%)
Query: 170 FEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDR--------------- 214
+ E + L I + + RL+ +E + + KRL+
Sbjct: 59 LDKDEEEEDLVPLSIFLGDN---RLITVRREPLPAVDEIRKRLENLGLGPKSPGDLLYLL 115
Query: 215 LQRLAEKVTREMKRVDGRLEELESRINEEARR--LDRLHPLDAKHNVDVLEHDLRQAEEN 272
L + ++ +++++ L+ELE + + L L L + ++ L L E
Sbjct: 116 LDSIVDRYFEILEKLEEELDELEDELEDSTTNELLREL--LRLRRSLVRLRRSLAPLREV 173
Query: 273 INTLFS-DVQTLREGRYPQASDLHKRVQKLHQRWVALRSLL 312
+N L S D + E DL +++L + LR L
Sbjct: 174 LNRLLSDDGPLIDEEEKEYLRDLLDELERLLEMAEILRERL 214
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 29.5 bits (67), Expect = 5.5
Identities = 19/105 (18%), Positives = 48/105 (45%), Gaps = 13/105 (12%)
Query: 196 AAHQEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDA 255
A +K+++L+ + + + +L+ E+ +E + L+ LE R+ + LDR
Sbjct: 45 AETLKKEALLEAKEE-VHKLRAELERELKERRN---ELQRLERRLLQREETLDR-----K 95
Query: 256 KHNVDVLEHDLRQAEENINTLFSDVQTLREGRYPQASDLHKRVQK 300
++D E +L + E+ ++ ++ E + +L ++
Sbjct: 96 MESLDKKEENLEKKEKELSNKEKNLDEKEE----ELEELIAEQRE 136
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.5 bits (67), Expect = 5.7
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 206 QDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDVLEHD 265
+ + + ++ EK+ +E+K ++ + ELE+ I E + ++RL P N D+
Sbjct: 82 KSLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIERLEPW---GNFDLDLSL 138
Query: 266 LR 267
L
Sbjct: 139 LL 140
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 29.5 bits (67), Expect = 5.8
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 10/77 (12%)
Query: 446 QRNAIRKALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKL 505
+R A++K E+ + S +L L +E+ E+ + + E + +AE+ +
Sbjct: 420 EREALKK----------EKDEASKERLEDLEKELAELEEEYADLEEQWKAEKAAIQGIQQ 469
Query: 506 FTEKASNLQSKLDEAER 522
E+ ++ +L++AER
Sbjct: 470 IKEEIEQVRLELEQAER 486
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 29.3 bits (66), Expect = 6.0
Identities = 24/114 (21%), Positives = 47/114 (41%), Gaps = 20/114 (17%)
Query: 453 ALNEDADKLLEEGDPSDPQLRRLRREMDEVNRLFDEFERRARAEEDMKNATKLFTEKASN 512
ALN+ + L E + + Q+ +L E+ E+ ER RAEE + +
Sbjct: 42 ALNKALEALEIELEDLENQVSQLESEIQEIR------ERIKRAEEKLSAVKDE--RELRA 93
Query: 513 LQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFESTLKNLMSDLEKREIQ 566
L ++ A+ ++SLE + + + L+ + DL++R +
Sbjct: 94 LNIEIQIAK------------ERINSLEDELAELMEEIEKLEKEIEDLKERLER 135
Score = 28.9 bits (65), Expect = 7.1
Identities = 23/112 (20%), Positives = 52/112 (46%), Gaps = 7/112 (6%)
Query: 212 LDRLQRLAEKVTREMKRVDGRLEELESRINEEARRLDRLHPLDAKHNVDV----LEHDLR 267
L+ L + E + E++ ++ ++ +LES I E R+ R + + L +++
Sbjct: 40 LEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQ 99
Query: 268 QAEENINTL---FSDVQTLREGRYPQASDLHKRVQKLHQRWVALRSLLHSRL 316
A+E IN+L +++ E + DL +R+++L + + L +
Sbjct: 100 IAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAEAEARLEEEV 151
>gnl|CDD|185339 PRK15442, PRK15442, beta-lactamase TEM; Provisional.
Length = 284
Score = 29.1 bits (65), Expect = 6.2
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 226 MKRVDGRLEELESRINEEARRLDRLHPLDAKHNVD 260
+ RVD E+L RI+ L P+ KH D
Sbjct: 77 LSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTD 111
>gnl|CDD|172640 PRK14151, PRK14151, heat shock protein GrpE; Provisional.
Length = 176
Score = 28.6 bits (64), Expect = 6.7
Identities = 31/99 (31%), Positives = 41/99 (41%), Gaps = 11/99 (11%)
Query: 492 RARAEEDMKNATKLFTEK-ASNLQSKLDEAERTLHSRINAPVPRDLDSLEHLVLQHKDFE 550
R RAE+D++ A K EK A +L +D ER L D E + + E
Sbjct: 54 RRRAEQDVEKAHKFALEKFAGDLLPVVDSLERGL----ELSSADD----EAIKPMREGVE 105
Query: 551 STLKNLMSDLEKREIQFSAVQDRGEALILQHHPAAKCIE 589
TLK L++ Q AV GE +HH A E
Sbjct: 106 LTLKMFQDTLKRY--QLEAVDPHGEPFNPEHHQAMAMQE 142
>gnl|CDD|201451 pfam00804, Syntaxin, Syntaxin. Syntaxins are the prototype family
of SNARE proteins. They usually consist of three main
regions - a C-terminal transmembrane region, a central
SNARE domain which is characteristic of and conserved in
all syntaxins (pfam05739), and an N-terminal domain that
is featured in this entry. This domain varies between
syntaxin isoforms; in syntaxin 1A it is found as three
alpha-helices with a left-handed twist. It may fold back
on the SNARE domain to allow the molecule to adopt a
'closed' configuration that prevents formation of the
core fusion complex - it thus has an auto-inhibitory
role. The function of syntaxins is determined by their
localisation. They are involved in neuronal exocytosis,
ER-Golgi transport and Golgi-endosome transport, for
example. They also interact with other proteins as well
as those involved in SNARE complexes. These include
vesicle coat proteins, Rab GTPases, and tethering
factors.
Length = 103
Score = 27.7 bits (62), Expect = 7.1
Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 165 DLTKYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRLDRLQRLAEKVTR 224
DL ++F++V E+ I I +N L H+ + + + + L+ L +++ +
Sbjct: 1 DLPEFFDEVEEI----REEIQKIRQNLEELQKLHKRILTAPDSDKELREELEELTQEIKQ 56
Query: 225 EMKRVDGRLEELESRINEEARR 246
+ + +L+ L+ E
Sbjct: 57 LARAIKKKLKSLQQLNKSEQGL 78
>gnl|CDD|144876 pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain. These
proteins contain several 22 residue repeats which form a
pair of alpha helices. This family includes:
Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein
E.
Length = 191
Score = 28.7 bits (65), Expect = 7.5
Identities = 26/107 (24%), Positives = 44/107 (41%), Gaps = 16/107 (14%)
Query: 218 LAEKVTREM----KRVDGRLEELESRINEEARRL-DRLHPLD-------AKHNVDVLEHD 265
L +++ R+ +++ EEL R+ + L RL P A+ ++ E
Sbjct: 83 LRKRLNRDAEELRRKLAPYAEELRDRLRQNVEALRARLGPYVEELRQKLAERLEELKESV 142
Query: 266 LRQAEENINTLFSDVQTLREGRYPQASDLHKR----VQKLHQRWVAL 308
AEE L V+ LRE P A DL ++ + L ++ L
Sbjct: 143 GPYAEEYKAQLSEQVEELREKLEPYAEDLREKLEPYAEDLKKQLAQL 189
>gnl|CDD|233004 TIGR00513, accA, acetyl-CoA carboxylase, carboxyl transferase,
alpha subunit. The enzyme acetyl-CoA carboxylase
contains a biotin carboxyl carrier protein or domain, a
biotin carboxylase, and a carboxyl transferase. This
model represents the alpha chain of the carboxyl
transferase for cases in which the architecture of the
protein is as in E. coli, in which the
carboxyltransferase portion consists of two
non-identical subnits, alpha and beta [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 316
Score = 29.0 bits (65), Expect = 7.7
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 178 IDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRL-DRLQRLAEKVTREMKRVDGRLEEL 236
+D E I +E L A +++D L +EI+RL R L +K+ +
Sbjct: 6 LDFEKPIAELEAKIESLRARSRDEDVDLSEEIERLEKRSVELTKKIFSNLG--------- 56
Query: 237 ESRINEEARRLDRLHPLD 254
+ + AR DR + LD
Sbjct: 57 AWQRLQLARHPDRPYTLD 74
>gnl|CDD|219955 pfam08657, DASH_Spc34, DASH complex subunit Spc34. The DASH
complex is a ~10 subunit microtubule-binding complex
that is transferred to the kinetochore prior to mitosis.
In Saccharomyces cerevisiae DASH forms both rings and
spiral structures on microtubules in vitro. Components
of the DASH complex, including Dam1, Duo1, Spc34, Dad1
and Ask1, are essential and connect the centromere to
the plus end of spindle microtubules.
Length = 255
Score = 28.6 bits (64), Expect = 8.2
Identities = 29/161 (18%), Positives = 57/161 (35%), Gaps = 29/161 (18%)
Query: 153 QRDKQRLQHIFQDLTKYFEDVGEVDIDPELHIDVIERNWSRLLAAHQEKDSILQDEIKRL 212
R R + T + EV + EL + + A S+L +EI
Sbjct: 95 NRRTTRKKGEGARGTVFNVPGPEVGTESELSSVPKADSEIKQSAVALVLGSVLTEEITVE 154
Query: 213 D----RLQRLAEKVT----------------REMKRVDGRLEELESRINEEARRLDRLH- 251
+ L R AE++ + + ELE+ I E+ R+L+ ++
Sbjct: 155 EFNVEVLLRGAEELCDVYPLPGAREKIETLRDRYNELSESIAELEAEIAEQKRQLEIMNI 214
Query: 252 --------PLDAKHNVDVLEHDLRQAEENINTLFSDVQTLR 284
+++ + ++ +R+ EE I L ++ L
Sbjct: 215 SSSSPSSDTSESEEDEIDIDELIRKEEEEIRELERQLRQLE 255
>gnl|CDD|239163 cd02762, MopB_1, The MopB_1 CD includes a group of related
uncharacterized bacterial molybdopterin-binding
oxidoreductase-like domains with a putative N-terminal
iron-sulfur [4Fe-4S] cluster binding site and
molybdopterin cofactor binding site. These members
belong to the molybdopterin_binding (MopB) superfamily
of proteins.
Length = 539
Score = 28.9 bits (65), Expect = 9.6
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 211 RLDRLQRLAEKVTREMKRVDGRLEEL--ESRINEEARRL 247
L Q +++ M+R G EE+ + +E A RL
Sbjct: 44 ALGDYQNDPDRLRTPMRRRGGSFEEIDWDEAFDEIAERL 82
>gnl|CDD|224934 COG2023, RPR2, RNase P subunit RPR2 [Translation, ribosomal
structure and biogenesis].
Length = 105
Score = 27.3 bits (61), Expect = 9.8
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 199 QEKDSILQDEIKRLDRLQRLAEKVTREMKRVDGRLEELESRINEEAR 245
K + + +R+D L LAE+ R + R +L RI+ + R
Sbjct: 1 ITKKRMKKIAAERIDYLYSLAEETFRTGPDLARRYVKLARRISMKYR 47
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 29.0 bits (65), Expect = 10.0
Identities = 67/375 (17%), Positives = 131/375 (34%), Gaps = 57/375 (15%)
Query: 185 DVIERNWSRLLAAHQEKDSILQDEIKRLDRL-------------QRLAEKVTREMKRVDG 231
D +++ SR A Q+ + + +L L +R+ E+ +
Sbjct: 253 DELQQEASRRQQALQQALAAEEKAQPQLAALSLAQPARQLRPHWERIQEQSAA-LAHTRQ 311
Query: 232 RLEELESRINEEARRLDRLHPLDAKHNVDVLEHDLRQ------AEENINTLFSDVQTLRE 285
++EE+ +R+ R+ A L+ + + +++ R
Sbjct: 312 QIEEVNTRLQSTMALRARIRH-HAAKQSAELQAQQQSLNTWLAEHDRFRQWNNELAGWRA 370
Query: 286 GRYPQASDLHKRVQKLHQRWVALRSLLHSRLVSPLASMSFPVVEERTVTRQTRTVMETRL 345
Q SD +++++ Q+ L++ L + V + R + + RL
Sbjct: 371 QFSQQTSD-REQLRQWQQQLTHAEQKLNALPAITLTLTADEVAAALAQHAEQRPLRQ-RL 428
Query: 346 VDTNTHFRALQEAIEWVKNKLAQIQEADYGSDLQGVQAEIAIHQREQNIIAQIQEADYGS 405
V AL I + +LAQ+Q A +Q V E QR + Q Y
Sbjct: 429 V-------ALHGQIVPQQKRLAQLQVA-----IQNVTQEQT--QRNAALNEMRQ--RYKE 472
Query: 406 DLQGVQAEIAIHQREQNI--IEQFHTRV------------EHCIAAKFLAMGAAQRNAIR 451
Q + I ++E I +E ++ H + A+ +
Sbjct: 473 KTQQLADVKTICEQEARIKDLEAQRAQLQAGQPCPLCGSTSHPAVEAYQALEPGVNQSRL 532
Query: 452 KALNEDADKLLEEGDPSDPQL----RRLRREMDEVNRLFDEFERRARAEEDMKNATKLFT 507
AL ++ KL EEG QL ++L+R+ E L E + + + + + +
Sbjct: 533 DALEKEVKKLGEEGAALRGQLDALTKQLQRDESEAQSLRQEEQALTQQWQAVCASLNITL 592
Query: 508 EKASNLQSKLDEAER 522
+ ++Q LD E
Sbjct: 593 QPQDDIQPWLDAQEE 607
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.131 0.378
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,049,264
Number of extensions: 3353003
Number of successful extensions: 5582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5230
Number of HSP's successfully gapped: 412
Length of query: 635
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 532
Effective length of database: 6,369,140
Effective search space: 3388382480
Effective search space used: 3388382480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.7 bits)