RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780567|ref|YP_003064980.1| hypothetical protein
CLIBASIA_02270 [Candidatus Liberibacter asiaticus str. psy62]
         (246 letters)



>gnl|CDD|169652 PRK09087, PRK09087, hypothetical protein; Validated.
          Length = 226

 Score =  275 bits (706), Expect = 7e-75
 Identities = 115/221 (52%), Positives = 146/221 (66%)

Query: 24  KEEQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83
             EQL  +F       RDDLLV  +   AV L+D WP+WPS VV+L GP GSGK+ LA+I
Sbjct: 4   APEQLPLNFSHDPAYGRDDLLVTESNRAAVSLVDHWPNWPSPVVVLAGPVGSGKTHLASI 63

Query: 84  WSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQLFHIINSIHQYDSSLLMT 143
           W +KS +          D+       PVL+EDID   F++T LFH+INS+ Q  +SLLMT
Sbjct: 64  WREKSDALLIHPNEIGSDAANAAAEGPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMT 123

Query: 144 ARTFPVSWGVCLPDLCSRLKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQ 203
           +R +P SW V LPDL SRLKAATVV+I  PDD  L +VI K+FADRQ+++D  +  Y+V 
Sbjct: 124 SRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVS 183

Query: 204 RMERSLVFAEKLVDKMDNLALSRGMGITRSLAAEVLKETQQ 244
           RMERSL  A+ +VD++D LAL R   ITR+LAAEVL E  Q
Sbjct: 184 RMERSLFAAQTIVDRLDRLALERKSRITRALAAEVLNEMGQ 224


>gnl|CDD|168630 PRK06620, PRK06620, hypothetical protein; Validated.
          Length = 214

 Score =  100 bits (251), Expect = 3e-22
 Identities = 58/220 (26%), Positives = 112/220 (50%), Gaps = 11/220 (5%)

Query: 26  EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSW----PSRVVILV-GPSGSGKSCL 80
           +Q  F F        D+ +V S+ +QA  +I +W       P +  +L+ GPS SGK+ L
Sbjct: 1   QQYIFRFTTSSKYHPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYL 60

Query: 81  ANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQLFHIINSIHQYDSSL 140
             IW + S +    +I    +  +++     ++EDI+  ++ +  L HI N I++    L
Sbjct: 61  TKIWQNLSNAYIIKDI--FFNEEILEKYNAFIIEDIE--NWQEPALLHIFNIINEKQKYL 116

Query: 141 LMTARTFPVSWGVCLPDLCSRLKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAY 200
           L+T+     ++   LPDL SR+K+   + ++ PDD+ ++ +I K F+   + I +++  +
Sbjct: 117 LLTSSDKSRNF--TLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDF 174

Query: 201 IVQRMERSLVFAEKLVDKMDNLALSRGMGITRSLAAEVLK 240
           ++  + R      ++++ ++  AL     IT SL  EVL 
Sbjct: 175 LLVNLPREYSKIIEILENINYFALISKRKITISLVKEVLN 214


>gnl|CDD|163254 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
           Members of this protein family are Hda (Homologous to
           DnaA). These proteins are about half the length of DnaA
           and homologous over length of Hda. In the model species
           Escherichia coli, the initiation of DNA replication
           requires DnaA bound to ATP rather than ADP; Hda helps
           facilitate the conversion of DnaA-ATP to DnaA-ADP.
          Length = 226

 Score = 72.6 bits (179), Expect = 8e-14
 Identities = 48/189 (25%), Positives = 77/189 (40%), Gaps = 14/189 (7%)

Query: 65  RVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVL----------LE 114
           R + L G SGSGKS L       +     S I   L + L      VL          L+
Sbjct: 39  RFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPL-AELAQADPEVLEGLEQADLVCLD 97

Query: 115 DIDLLDFNDT---QLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKIS 171
           D++ +         LFH+ N + +    LL+  R  P    + LPDL +RL    V ++ 
Sbjct: 98  DVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLP 157

Query: 172 LPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGIT 231
              D+     +    A R + +  ++A Y+++   R +     L+D +D  +L+    IT
Sbjct: 158 PLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAKRKIT 217

Query: 232 RSLAAEVLK 240
                EVL 
Sbjct: 218 IPFVKEVLA 226


>gnl|CDD|181578 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
          Length = 227

 Score = 51.1 bits (123), Expect = 3e-07
 Identities = 43/188 (22%), Positives = 85/188 (45%), Gaps = 12/188 (6%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKS----RSTRFSNIAKSLDSILIDTRKPVL-LEDID 117
             R   L G +GSG+S L       +    R+ R+ + A  L +   D    +  ++D++
Sbjct: 41  ADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLLAFDFDPEAELYAVDDVE 100

Query: 118 LLDFNDTQ--LFHIINSIHQY-DSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKI-SLP 173
            LD +  Q  LF++ N +  +   +LL+     P++  +   DL +RL    V ++  L 
Sbjct: 101 RLD-DAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPL-REDLRTRLGWGLVYELKPLS 158

Query: 174 DDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITRS 233
           D D +   +    A+R + +  ++  Y++    R +     L+D +D  +L +   +T  
Sbjct: 159 DADKIA-ALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQKRPVTLP 217

Query: 234 LAAEVLKE 241
           L  E+L +
Sbjct: 218 LLREMLAQ 225


>gnl|CDD|168147 PRK05642, PRK05642, DNA replication initiation factor; Validated.
          Length = 234

 Score = 48.7 bits (116), Expect = 1e-06
 Identities = 54/211 (25%), Positives = 94/211 (44%), Gaps = 22/211 (10%)

Query: 47  SAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID 106
           +A+    RL ++   W   ++ L G  G G+S L  + +   R  +    A  L    + 
Sbjct: 28  AALGYVERLCEADAGWTESLIYLWGKDGVGRSHL--LQAACLRFEQRGEPAVYLPLAELL 85

Query: 107 TRKPVLLEDI---DLLDFNDTQ-----------LFHIINSIHQYDSSLLMTARTFPVSWG 152
            R P LL+++   +L+  +D             LFH+ N +      LL+ A   P    
Sbjct: 86  DRGPELLDNLEQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELP 145

Query: 153 VCLPDLCSRLKAATVVKI-SLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVF 211
           + LPDL SRL  A V ++  L D+D L  + ++  + R + +  ++  +I+ R  RS+  
Sbjct: 146 IKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRA-SRRGLHLTDEVGHFILTRGTRSMSA 204

Query: 212 AEKLVDKMDNLALSRGMGITRSLAAEVLKET 242
              L++++D  +L       R L    LKET
Sbjct: 205 LFDLLERLDQASLQA----QRKLTIPFLKET 231


>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
          Length = 233

 Score = 47.5 bits (113), Expect = 3e-06
 Identities = 50/191 (26%), Positives = 88/191 (46%), Gaps = 20/191 (10%)

Query: 67  VILVGPSGSGKSCLA-NIWSDKSRSTRFS----------NIAKSLDSILIDTRKPVLLED 115
           + L GP+G+GK+ LA  + +   ++ R S           +  +L+++  + R  V L+ 
Sbjct: 44  LYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRDALEAL--EGRSLVALDG 101

Query: 116 IDLLDFN---DTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKISL 172
           ++ +      +  LF   N       +LL TAR  P    + LPDL SRL  A  ++I L
Sbjct: 102 LESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRL--AQCIRIGL 159

Query: 173 P--DDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGI 230
           P  DD     V+ +    R + +D+    +++   ER L     L+D++D  +L+    +
Sbjct: 160 PVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKRRV 219

Query: 231 TRSLAAEVLKE 241
           T      VL+E
Sbjct: 220 TVPFLRRVLEE 230


>gnl|CDD|168719 PRK06893, PRK06893, DNA replication initiation factor; Validated.
          Length = 229

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 31/134 (23%), Positives = 65/134 (48%), Gaps = 4/134 (2%)

Query: 111 VLLEDIDLLDFNDT---QLFHIINSIHQYDSSLLM-TARTFPVSWGVCLPDLCSRLKAAT 166
           V L+D+  +  N+     +F + N I +   +LL+ +A   P +  + LPDL SRL    
Sbjct: 95  VCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGE 154

Query: 167 VVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSR 226
           + +++   D+    V+ +    R I +  ++A ++++R++R +      +D +D  +L  
Sbjct: 155 IYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQA 214

Query: 227 GMGITRSLAAEVLK 240
              +T     E+L 
Sbjct: 215 QRKLTIPFVKEILG 228


>gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
           DnaA is involved in DNA biosynthesis; initiation of
           chromosome replication and can also be transcription
           regulator. The C-terminal of the family hits the pfam
           bacterial DnaA (bac_dnaA) domain family. For a review,
           see Kaguni (2006).
          Length = 405

 Score = 37.9 bits (89), Expect = 0.002
 Identities = 38/152 (25%), Positives = 61/152 (40%), Gaps = 35/152 (23%)

Query: 113 LEDIDLLDFNDTQ-----------LFHIINSIHQYDSSLLMTARTFPVSWGVCLPD---- 157
              +DLL  +D Q            FH  N++H+    +++T+   P      LP     
Sbjct: 197 YRSVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKE----LPGLEER 252

Query: 158 LCSRLKAATVVKISLPDDDFLE---KVIVKMFADRQIFIDKKLAAYIVQRME---RSLVF 211
           L SR +   VV I  PD   LE    ++ K   +  + +  ++  +I + +    R L  
Sbjct: 253 LRSRFEWGLVVDIEPPD---LETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEG 309

Query: 212 AEKLVDKMDNLALSRGMG--ITRSLAAEVLKE 241
           A   +     LA +   G  IT  LA E LK+
Sbjct: 310 ALNRL-----LAYASLTGKPITLELAKEALKD 336


>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
            This protein is related to a Proteobacterial ATP
           transporter that exports lipid A and to eukaryotic
           P-glycoproteins.
          Length = 576

 Score = 35.8 bits (83), Expect = 0.009
 Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 13/55 (23%)

Query: 26  EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCL 80
           EQ+ F++P     +R D      +   VR        P   V LVGPSG+GKS L
Sbjct: 341 EQVNFAYP-----ARPDQPALDGLNLTVR--------PGETVALVGPSGAGKSTL 382


>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
           MsbA.  This family consists of a single polypeptide
           chain transporter in the ATP-binding cassette (ABC)
           transporter family, MsbA, which exports lipid A. It may
           also act in multidrug resistance. Lipid A, a part of
           lipopolysaccharide, is found in the outer leaflet of the
           outer membrane of most Gram-negative bacteria. Members
           of this family are restricted to the Proteobacteria
           (although lipid A is more broadly distributed) and often
           are clustered with lipid A biosynthesis genes.
          Length = 571

 Score = 35.5 bits (82), Expect = 0.012
 Identities = 26/71 (36%), Positives = 30/71 (42%), Gaps = 15/71 (21%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKS---LDSI------LIDTRKPVLL 113
           P   V LVG SGSGKS L N+        RF         LD        L   R+ V L
Sbjct: 357 PGETVALVGRSGSGKSTLVNLI------PRFYEPDSGQILLDGHDLADYTLASLRRQVAL 410

Query: 114 EDIDLLDFNDT 124
              D++ FNDT
Sbjct: 411 VSQDVVLFNDT 421


>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
           Provisional.
          Length = 582

 Score = 33.8 bits (78), Expect = 0.040
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 8/40 (20%)

Query: 67  VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID 106
           V LVG SGSGKS +AN+       TRF +I +    IL+D
Sbjct: 372 VALVGRSGSGKSTIANLL------TRFYDIDEG--EILLD 403


>gnl|CDD|162132 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein. 
          Length = 711

 Score = 33.5 bits (77), Expect = 0.055
 Identities = 14/19 (73%), Positives = 15/19 (78%)

Query: 63  PSRVVILVGPSGSGKSCLA 81
           P  VV LVGPSGSGKS +A
Sbjct: 506 PGEVVALVGPSGSGKSTVA 524


>gnl|CDD|178750 PLN03211, PLN03211, ABC transporter G-25; Provisional.
          Length = 659

 Score = 33.3 bits (76), Expect = 0.056
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 6/48 (12%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110
           P  ++ ++GPSGSGKS L N  + + +   F+       +IL + RKP
Sbjct: 93  PGEILAVLGPSGSGKSTLLNALAGRIQGNNFTG------TILANNRKP 134


>gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed.
          Length = 356

 Score = 33.0 bits (76), Expect = 0.067
 Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 45  VHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN 82
           V +   + + ++ +W S   + V L+G SG GKS L N
Sbjct: 177 VSALDGEGLDVLAAWLS-GGKTVALLGSSGVGKSTLVN 213


>gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein;
           Reviewed.
          Length = 450

 Score = 32.8 bits (76), Expect = 0.075
 Identities = 37/154 (24%), Positives = 61/154 (39%), Gaps = 43/154 (27%)

Query: 115 DIDLLDFNDTQ-----------LFHIINSIHQYDSSLLMTARTFPVSWGVCLPD----LC 159
            +D+L  +D Q            FH  N++H+    +++T+   P      LP     L 
Sbjct: 211 SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKE----LPGLEERLR 266

Query: 160 SRLKAATVVKISLPDDDFLE---KVIVKMFADRQIFIDKKLAAYIVQRME---RSLVFAE 213
           SR +    V I  PD   LE    ++ K   +  I +  ++  +I + +    R L   E
Sbjct: 267 SRFEWGLTVDIEPPD---LETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVREL---E 320

Query: 214 ----KLVDKMDNLALSRGMG--ITRSLAAEVLKE 241
               +L+      A +   G  IT  LA E LK+
Sbjct: 321 GALNRLI------AYASLTGKPITLELAKEALKD 348


>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
          Provisional.
          Length = 482

 Score = 33.0 bits (76), Expect = 0.083
 Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 48 AIEQAVRLIDSWPS-WPSRVVILVGPSGSGKSCLA 81
          A EQ    I+SW    P + ++L GP G GK+ LA
Sbjct: 22 AKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLA 56


>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
          Reviewed.
          Length = 240

 Score = 32.8 bits (75), Expect = 0.083
 Identities = 11/15 (73%), Positives = 14/15 (93%)

Query: 66 VVILVGPSGSGKSCL 80
          VV+++GPSGSGKS L
Sbjct: 29 VVVIIGPSGSGKSTL 43


>gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter
           membrane\ATP-binding components; Provisional.
          Length = 592

 Score = 32.8 bits (75), Expect = 0.096
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 17/59 (28%)

Query: 26  EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSR-VVILVGPSGSGKSCLANI 83
           + + F++       RDD LV   I  +V         PSR  V LVG +GSGKS LA++
Sbjct: 344 DNVSFAY-------RDDNLVLQNINLSV---------PSRGFVALVGHTGSGKSTLASL 386


>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
           activities.  AAA - ATPases associated with a variety of
           cellular activities. This profile/alignment only detects
           a fraction of this vast family. The poorly conserved
           N-terminal helix is missing from the alignment.
          Length = 148

 Score = 32.7 bits (74), Expect = 0.097
 Identities = 16/63 (25%), Positives = 28/63 (44%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122
           P  V+++VGP GSGK+ LA   + +        I    + IL +    +LL  +     +
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 123 DTQ 125
            + 
Sbjct: 61  GSG 63


>gnl|CDD|181224 PRK08084, PRK08084, DNA replication initiation factor; Provisional.
          Length = 235

 Score = 32.3 bits (74), Expect = 0.13
 Identities = 27/117 (23%), Positives = 58/117 (49%), Gaps = 3/117 (2%)

Query: 126 LFHIINSI-HQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKIS-LPDDDFLEKVIV 183
           +F + N I     + LL+T    P    + LPDL SRL    + K+  L D++ L+ + +
Sbjct: 119 IFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQL 178

Query: 184 KMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITRSLAAEVLK 240
           +    R   + + +  ++++R++R +      +D++D  +++    +T     E+LK
Sbjct: 179 RA-RLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRKLTIPFVKEILK 234


>gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit,
          DevA family.  Members of this protein family are found
          mostly in the Cyanobacteria, but also in the
          Planctomycetes. Cyanobacterial examples are involved in
          heterocyst formation, by which some fraction of members
          of the colony undergo a developmental change and become
          capable of nitrogen fixation. The DevBCA proteins are
          thought export of either heterocyst-specific
          glycolipids or an enzyme essential for formation of the
          laminated layer found in heterocysts.
          Length = 220

 Score = 32.3 bits (74), Expect = 0.13
 Identities = 12/18 (66%), Positives = 14/18 (77%)

Query: 63 PSRVVILVGPSGSGKSCL 80
          P  +VIL GPSGSGK+ L
Sbjct: 30 PGEIVILTGPSGSGKTTL 47


>gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
           transporter, PrtD family.  Type I protein secretion is a
           system in some Gram-negative bacteria to export proteins
           (often proteases) across both inner and outer membranes
           to the extracellular medium. This is one of three
           proteins of the type I secretion apparatus. Targeted
           proteins are not cleaved at the N-terminus, but rather
           carry signals located toward the extreme C-terminus to
           direct type I secretion.
          Length = 544

 Score = 31.9 bits (73), Expect = 0.15
 Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%)

Query: 63  PSRVVILVGPSGSGKSCLAN----IWSDKSRSTRF 93
               + ++GPSGSGKS LA     IW   S S R 
Sbjct: 343 AGEALAIIGPSGSGKSTLARLIVGIWPPTSGSVRL 377


>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24.  This family is based
           on the phylogenomic analysis of JA Eisen (1999, Ph.D.
           Thesis, Stanford University).
          Length = 637

 Score = 31.9 bits (72), Expect = 0.16
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 5/48 (10%)

Query: 42  DLLVH----SAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWS 85
           +L VH      +E  +       + P R++++ GPSG GKS    I S
Sbjct: 85  ELAVHKKKIEEVETWL-KAQVLENAPKRILLITGPSGCGKSTTIKILS 131


>gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases.  Rab GTPases are
          implicated in vesicle trafficking.
          Length = 164

 Score = 31.7 bits (73), Expect = 0.20
 Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 5/30 (16%)

Query: 67 VILVGPSGSGKSCL-----ANIWSDKSRST 91
          +IL+G SG GKS L        +S++ +ST
Sbjct: 3  IILIGDSGVGKSSLLSRFTDGKFSEQYKST 32


>gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
          transferase; Reviewed.
          Length = 307

 Score = 31.3 bits (72), Expect = 0.23
 Identities = 9/17 (52%), Positives = 15/17 (88%)

Query: 65 RVVILVGPSGSGKSCLA 81
          +V+++VGP+ SGK+ LA
Sbjct: 5  KVIVIVGPTASGKTALA 21


>gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC
           transporter, peptidase/ATP-binding protein.  This
           protein describes an multidomain ABC transporter subunit
           that is one of three protein families associated with
           some regularity with a distinctive family of putative
           bacteriocins. It includes a bacteriocin-processing
           peptidase domain at the N-terminus. Model TIGR03793
           describes a conserved propeptide region for this
           bacteriocin family, unusual because it shows obvious
           homology a region of the enzyme nitrile hydratase up to
           the classic Gly-Gly cleavage motif. This family is
           therefore predicted to be a subunit of a bacteriocin
           processing and export system characteristic to this
           system that we designate NHPM, Nitrile Hydratase
           Propeptide Microcin.
          Length = 710

 Score = 31.1 bits (71), Expect = 0.28
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 63  PSRVVILVGPSGSGKSCLANI 83
           P + V LVG SGSGKS +A +
Sbjct: 504 PGQRVALVGGSGSGKSTIAKL 524


>gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.
           Unfortunately, the gene symbol nomenclature adopted
           based on this operon in B. subtilis assigns cydC to the
           third gene in the operon where this gene is actually
           homologous to the E. coli cydD gene. We have chosen to
           name all homologs in this family in accordance with the
           precedence of publication of the E. coli name, CydD.
          Length = 529

 Score = 30.7 bits (70), Expect = 0.31
 Identities = 13/20 (65%), Positives = 14/20 (70%)

Query: 63  PSRVVILVGPSGSGKSCLAN 82
           P   V LVGPSG+GKS L N
Sbjct: 347 PGERVALVGPSGAGKSTLLN 366


>gnl|CDD|162807 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein
          PhnK.  Members of this family are the PhnK protein of
          C-P lyase systems for utilization of phosphonates.
          These systems resemble phosphonatase-based systems in
          having a three component ABC transporter, where
          TIGR01097 is the permease, TIGR01098 is the
          phosphonates binding protein, and TIGR02315 is the
          ATP-binding cassette (ABC) protein. They differ,
          however, in having, typically, ten or more additional
          genes, many of which are believed to form a
          membrane-associated complex. This protein (PhnK) and
          the adjacent-encoded PhnL resemble transporter
          ATP-binding proteins but are suggested, based on
          mutatgenesis studies, to be part of this complex rather
          than part of a transporter per se.
          Length = 253

 Score = 31.0 bits (70), Expect = 0.33
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 62 WPSRVVILVGPSGSGKSCLANIWSDK 87
          +P  V+ +VG SGSGKS L    + +
Sbjct: 27 YPGEVLGIVGESGSGKSTLLGCLAGR 52


>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
          Length = 298

 Score = 30.9 bits (71), Expect = 0.33
 Identities = 20/91 (21%), Positives = 28/91 (30%), Gaps = 27/91 (29%)

Query: 34  RCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN----------- 82
             L +S  +      ++    L         +V +L G SG GKS L N           
Sbjct: 143 DVLELSAKEGEGLDELKP--LLAG-------KVTVLAGQSGVGKSTLLNALAPDLELKTG 193

Query: 83  -IWSDKSRS----TRFSN-IAKSLDSILIDT 107
            I S+        T            +LIDT
Sbjct: 194 EI-SEALGRGKHTTTHVELYDLPGGGLLIDT 223


>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
          Provisional.
          Length = 258

 Score = 30.7 bits (70), Expect = 0.36
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 62 WPSRVVILVGPSGSGKSCLAN 82
          +P  V+ +VG SGSGK+ L N
Sbjct: 30 YPGEVLGIVGESGSGKTTLLN 50


>gnl|CDD|178430 PLN02836, PLN02836, 3-oxoacyl-[acyl-carrier-protein] synthase.
          Length = 437

 Score = 30.5 bits (69), Expect = 0.37
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 6/59 (10%)

Query: 37 GISRDDL-LVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGK-SCLANIWSDKSRSTRF 93
           +++DDL +     E  +  +D  PS   RV  LV P G+G       +W +   S+RF
Sbjct: 39 ALTQDDLKMKSEDEETQLYTLDQLPS---RVAALV-PRGTGPGDFDEELWLNSRSSSRF 93


>gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed.
          Length = 352

 Score = 30.8 bits (70), Expect = 0.39
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 49  IEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN 82
           +E  + L        +++ ++ GPSG GKS L N
Sbjct: 157 VETGIGLEALLEQLRNKITVVAGPSGVGKSSLIN 190


>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
          domain-containing protein; Reviewed.
          Length = 229

 Score = 30.3 bits (69), Expect = 0.47
 Identities = 9/25 (36%), Positives = 13/25 (52%)

Query: 65 RVVILVGPSGSGKSCLANIWSDKSR 89
           +V + GP G+GKS LA       +
Sbjct: 34 TIVGIAGPPGAGKSTLAEFLEALLQ 58


>gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter
           membrane/ATP-binding component; Reviewed.
          Length = 588

 Score = 29.8 bits (68), Expect = 0.62
 Identities = 10/16 (62%), Positives = 13/16 (81%)

Query: 67  VILVGPSGSGKSCLAN 82
           + LVGPSG+GK+ L N
Sbjct: 379 IALVGPSGAGKTSLLN 394


>gnl|CDD|182443 PRK10418, nikD, nickel transporter ATP-binding protein NikD;
          Provisional.
          Length = 254

 Score = 30.1 bits (68), Expect = 0.64
 Identities = 13/19 (68%), Positives = 14/19 (73%), Gaps = 2/19 (10%)

Query: 65 RVVILVGPSGSGKS--CLA 81
          RV+ LVG SGSGKS  C A
Sbjct: 30 RVLALVGGSGSGKSLTCAA 48


>gnl|CDD|183258 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
          subunit; Provisional.
          Length = 356

 Score = 29.8 bits (68), Expect = 0.65
 Identities = 10/14 (71%), Positives = 12/14 (85%)

Query: 67 VILVGPSGSGKSCL 80
          ++LVGPSG GKS L
Sbjct: 33 IVLVGPSGCGKSTL 46


>gnl|CDD|182226 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
          Length = 186

 Score = 29.7 bits (67), Expect = 0.66
 Identities = 9/18 (50%), Positives = 13/18 (72%)

Query: 63 PSRVVILVGPSGSGKSCL 80
            +++ L+GPSGSGK  L
Sbjct: 1  MGKLIWLMGPSGSGKDSL 18


>gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional.
          Length = 205

 Score = 29.7 bits (68), Expect = 0.69
 Identities = 10/30 (33%), Positives = 18/30 (60%)

Query: 65 RVVILVGPSGSGKSCLANIWSDKSRSTRFS 94
           +++L GPSG+GKS L     ++  + + S
Sbjct: 6  LLIVLSGPSGAGKSTLVKALLERDPNLQLS 35


>gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM bacteriocin system ABC
           transporter, ATP-binding protein.  Members of this
           protein family are ABC transporter ATP-binding subunits,
           part of a three-gene putative bacteriocin transport
           operon. The other subunits include another ATP-binding
           subunit (TIGR03796), which has an N-terminal propeptide
           cleavage domain, and an HlyD homolog (TIGR03794). In a
           number of genomes, a conserved propeptide sequence with
           a classic Gly-Gly motif.
          Length = 686

 Score = 29.5 bits (67), Expect = 0.72
 Identities = 12/18 (66%), Positives = 13/18 (72%)

Query: 63  PSRVVILVGPSGSGKSCL 80
           P   V +VGPSGSGKS L
Sbjct: 478 PGEFVAIVGPSGSGKSTL 495


>gnl|CDD|184133 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
          Length = 258

 Score = 29.4 bits (67), Expect = 0.80
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 63 PSRVVILVGPSGSGKSCL 80
          P  VV ++GP+G+GKS L
Sbjct: 27 PGEVVAILGPNGAGKSTL 44


>gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
          Length = 288

 Score = 29.7 bits (68), Expect = 0.80
 Identities = 10/16 (62%), Positives = 13/16 (81%)

Query: 63 PSRVVILVGPSGSGKS 78
          P R+VI+ G SG+GKS
Sbjct: 5  PMRLVIVTGLSGAGKS 20


>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit.  The
           gene pair cydCD encodes an ABC-family transporter in
           which each gene contains an N-terminal membrane-spanning
           domain (pfam00664) and a C-terminal ATP-binding domain
           (pfam00005). In E. coli these genes were discovered as
           mutants which caused the terminal heme-copper oxidase
           complex cytochrome bd to fail to assemble. Recent work
           has shown that the transporter is involved in export of
           redox-active thiol compounds such as cysteine and
           glutathione. The linkage to assembly of the cytochrome
           bd complex is further supported by the conserved operon
           structure found outside the gammaproteobacteria
           (cydABCD) containing both the transporter and oxidase
           genes components. The genes used as the seed members for
           this model are all either found in the
           gammproteobacterial context or the CydABCD context. All
           members of this family scoring above trusted at the time
           of its creation were from genomes which encode a
           cytochrome bd complex.
          Length = 529

 Score = 29.3 bits (66), Expect = 0.91
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 63  PSRVVILVGPSGSGKSCLANIW 84
           P   V ++GPSGSGKS L  + 
Sbjct: 360 PGERVAILGPSGSGKSTLLMLL 381


>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
          Length = 172

 Score = 29.3 bits (66), Expect = 0.92
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 65 RVVILVGPSGSGKSCLAN 82
            V++ G SGSGK+ LA 
Sbjct: 16 ITVLIDGRSGSGKTTLAG 33


>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
          Length = 175

 Score = 29.4 bits (67), Expect = 0.93
 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 12/45 (26%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107
               ++L+G  G+GKS +  +            +AK L    IDT
Sbjct: 3   KGPNIVLIGFMGAGKSTIGRL------------LAKRLGYDFIDT 35


>gnl|CDD|132490 TIGR03449, mycothiol_MshA, UDP-N-acetylglucosamine:
           1L-myo-inositol-1-phosphate
           1-alpha-D-N-acetylglucosaminyltransferase.  Members of
           this protein family, found exclusively in the
           Actinobacteria, are MshA, the glycosyltransferase of
           mycothiol biosynthesis. Mycothiol replaces glutathione
           in these species.
          Length = 405

 Score = 29.3 bits (66), Expect = 0.94
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 4/35 (11%)

Query: 42  DLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSG 76
           D+L+ +  E    L+D  P    RV+++ GPSGSG
Sbjct: 235 DVLLRAVAE----LLDRDPDRNLRVIVVGGPSGSG 265


>gnl|CDD|178697 PLN03152, PLN03152, hypothetical protein; Provisional.
          Length = 241

 Score = 29.4 bits (66), Expect = 0.94
 Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 33 PRCL-GISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKS 88
          P    G SR D ++H+A   A  L    P  PS    L  PS   K  L+ I + KS
Sbjct: 25 PLSRCGASRRDFILHTASLCASSLAAQNPLPPS----LADPSKPSKPLLSGIANTKS 77


>gnl|CDD|163352 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
          transporter, lactococcin 972 group.  A gene pair with a
          fairly wide distribution consists of a polypeptide
          related to the lactococcin 972 (see TIGR01653) and
          multiple-membrane-spanning putative immunity protein
          (see TIGR01654). This model represents a small clade
          within the ABC transporters that regularly are found
          adjacent to these bacteriocin system gene pairs and are
          likely serve as export proteins.
          Length = 206

 Score = 29.1 bits (66), Expect = 0.95
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 66 VVILVGPSGSGKSCLANI 83
          +  ++G SGSGKS L NI
Sbjct: 26 MYAIIGESGSGKSTLLNI 43


>gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease
          protein; Provisional.
          Length = 648

 Score = 29.3 bits (66), Expect = 0.99
 Identities = 12/17 (70%), Positives = 13/17 (76%)

Query: 67 VILVGPSGSGKSCLANI 83
          V +VG SGSGKS L NI
Sbjct: 37 VAIVGASGSGKSTLMNI 53


>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
          Provisional.
          Length = 232

 Score = 29.2 bits (66), Expect = 1.0
 Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 1/19 (5%)

Query: 65 RVVILVGPSGSGKSCLANI 83
          RV IL GPSG+GKS L N+
Sbjct: 27 RVAIL-GPSGAGKSTLLNL 44


>gnl|CDD|183063 PRK11264, PRK11264, putative amino-acid ABC transporter
          ATP-binding protein YecC; Provisional.
          Length = 250

 Score = 28.9 bits (65), Expect = 1.1
 Identities = 11/18 (61%), Positives = 14/18 (77%)

Query: 63 PSRVVILVGPSGSGKSCL 80
          P  VV ++GPSGSGK+ L
Sbjct: 28 PGEVVAIIGPSGSGKTTL 45


>gnl|CDD|130034 TIGR00960, 3a0501s02, Type II (General) Secretory Pathway (IISP)
          Family protein. 
          Length = 216

 Score = 28.9 bits (65), Expect = 1.3
 Identities = 11/30 (36%), Positives = 15/30 (50%)

Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTR 92
             +V LVG SG+GKS    +     + TR
Sbjct: 28 KGEMVFLVGHSGAGKSTFLKLILGIEKPTR 57


>gnl|CDD|167016 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
          Length = 1809

 Score = 29.0 bits (65), Expect = 1.3
 Identities = 12/19 (63%), Positives = 14/19 (73%)

Query: 63 PSRVVILVGPSGSGKSCLA 81
          P  +V+L G SGSGKS LA
Sbjct: 25 PREIVLLTGVSGSGKSSLA 43


>gnl|CDD|178349 PLN02748, PLN02748, tRNA dimethylallyltransferase.
          Length = 468

 Score = 28.7 bits (64), Expect = 1.3
 Identities = 11/17 (64%), Positives = 16/17 (94%)

Query: 65 RVVILVGPSGSGKSCLA 81
          +VV+++GP+GSGKS LA
Sbjct: 23 KVVVVMGPTGSGKSKLA 39


>gnl|CDD|178800 PRK00023, cmk, cytidylate kinase; Provisional.
          Length = 225

 Score = 28.9 bits (66), Expect = 1.3
 Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 12/37 (32%)

Query: 71  GPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107
           GP+GSGK  +A I            +AK L    +DT
Sbjct: 11  GPAGSGKGTVAKI------------LAKKLGFHYLDT 35


>gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
           Provisional.
          Length = 412

 Score = 29.0 bits (66), Expect = 1.4
 Identities = 9/15 (60%), Positives = 14/15 (93%)

Query: 67  VILVGPSGSGKSCLA 81
           ++L+GP+GSGK+ LA
Sbjct: 111 ILLIGPTGSGKTLLA 125


>gnl|CDD|161968 TIGR00630, uvra, excinuclease ABC, A subunit.  This family is
          based on the phylogenomic analysis of JA Eisen (1999,
          Ph.D. Thesis, Stanford University).
          Length = 924

 Score = 28.8 bits (65), Expect = 1.4
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 63 PSRVVILVGPSGSGKSCLA 81
            ++V++ G SGSGKS LA
Sbjct: 21 RDKLVVITGLSGSGKSSLA 39



 Score = 26.1 bits (58), Expect = 9.3
 Identities = 9/16 (56%), Positives = 10/16 (62%)

Query: 67  VILVGPSGSGKSCLAN 82
             + G SGSGKS L N
Sbjct: 636 TCITGVSGSGKSTLIN 651


>gnl|CDD|178984 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
          Length = 943

 Score = 28.5 bits (65), Expect = 1.5
 Identities = 11/16 (68%), Positives = 11/16 (68%), Gaps = 1/16 (6%)

Query: 66 VVILVGPSGSGKSCLA 81
          VV   G SGSGKS LA
Sbjct: 29 VVF-TGLSGSGKSSLA 43


>gnl|CDD|162636 TIGR01978, sufC, FeS assembly ATPase SufC.  SufC is part of the
          SUF system, shown in E. coli to consist of six proteins
          and believed to act in Fe-S cluster formation during
          oxidative stress. SufC forms a complex with SufB and
          SufD. SufC belongs to the ATP-binding cassette
          transporter family (pfam00005) but is no longer thought
          to be part of a transporter. The complex is reported as
          cytosolic (PubMed:12554644) or associated with the
          membrane (PubMed:11943156). The SUF system also
          includes a cysteine desulfurase (SufS, enhanced by
          SufE) and a probable iron-sulfur cluster assembly
          scaffold protein, SufA.
          Length = 243

 Score = 28.8 bits (65), Expect = 1.5
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 66 VVILVGPSGSGKSCLANI 83
          +  ++GP+GSGKS L+  
Sbjct: 28 IHAIMGPNGSGKSTLSKT 45


>gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein;
          Provisional.
          Length = 252

 Score = 28.6 bits (64), Expect = 1.6
 Identities = 11/19 (57%), Positives = 15/19 (78%)

Query: 62 WPSRVVILVGPSGSGKSCL 80
          +P+ +  L+GPSGSGKS L
Sbjct: 29 YPNEITALIGPSGSGKSTL 47


>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily).  This
          Pfam entry includes some of the AAA proteins not
          detected by the pfam00004 model.
          Length = 139

 Score = 28.4 bits (64), Expect = 1.6
 Identities = 11/15 (73%), Positives = 13/15 (86%)

Query: 67 VILVGPSGSGKSCLA 81
          V+LVGP G+GKS LA
Sbjct: 2  VLLVGPPGTGKSELA 16


>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus.  This family consists of the
          C-terminal region of several eukaryotic and archaeal
          RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
          or TIP49b) proteins. The N-terminal domain contains the
          pfam00004 domain. In zebrafish, the liebeskummer (lik)
          mutation, causes development of hyperplastic embryonic
          hearts. lik encodes Reptin, a component of a
          DNA-stimulated ATPase complex. Beta-catenin and Pontin,
          a DNA-stimulated ATPase that is often part of complexes
          with Reptin, are in the same genetic pathways. The
          Reptin/Pontin ratio serves to regulate heart growth
          during development, at least in part via the
          beta-catenin pathway. TBP-interacting protein 49
          (TIP49) was originally identified as a TBP-binding
          protein, and two related proteins are encoded by
          individual genes, tip49a and b. Although the function
          of this gene family has not been elucidated, they are
          supposed to play a critical role in nuclear events
          because they interact with various kinds of nuclear
          factors and have DNA helicase activities.TIP49a has
          been suggested to act as an autoantigen in some
          patients with autoimmune diseases.
          Length = 395

 Score = 28.4 bits (64), Expect = 1.7
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 65 RVVILVGPSGSGKSCLA 81
          R V++ GP G+GK+ LA
Sbjct: 51 RAVLIAGPPGTGKTALA 67


>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
           subunit 1/adenylylsulfate kinase protein; Provisional.
          Length = 632

 Score = 28.4 bits (64), Expect = 1.7
 Identities = 10/18 (55%), Positives = 11/18 (61%)

Query: 65  RVVILVGPSGSGKSCLAN 82
             V   G SGSGKS +AN
Sbjct: 461 ATVWFTGLSGSGKSTIAN 478


>gnl|CDD|163222 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.
          Length = 852

 Score = 28.4 bits (64), Expect = 1.8
 Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 7/36 (19%)

Query: 47  SAIEQAVR-----LIDSWPSWPSRVVILVGPSGSGK 77
            AI + +R     L D  P  P  V +LVGPSG GK
Sbjct: 576 EAIAERIRTARAGLED--PRKPLGVFLLVGPSGVGK 609


>gnl|CDD|162806 TIGR02322, phosphon_PhnN, phosphonate metabolism
          protein/1,5-bisphosphokinase (PRPP-forming) PhnN.
          Members of this family resemble PhnN of phosphonate
          utilization operons, where different such operons
          confer the ability to use somewhat different profiles
          of C-P bond-containing compounds (see PubMed:15231805),
          including phosphites as well as phosphonates. PhnN in
          E. coli shows considerable homology to guanylate
          kinases (EC 2.7.4.8), and has actually been shown to
          act as a ribose 1,5-bisphosphokinase (PRPP forming).
          This suggests an analogous kinase reaction for
          phosphonate metabolism, converting
          5-phosphoalpha-1-(methylphosphono)ribose to
          methylphosphono-PRPP.
          Length = 179

 Score = 28.1 bits (63), Expect = 1.9
 Identities = 9/16 (56%), Positives = 13/16 (81%)

Query: 65 RVVILVGPSGSGKSCL 80
          R++ +VGPSG+GK  L
Sbjct: 2  RLIYVVGPSGAGKDTL 17


>gnl|CDD|162558 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
           transporter, HlyB family.  Type I protein secretion is a
           system in some Gram-negative bacteria to export proteins
           (often proteases) across both inner and outer membranes
           to the extracellular medium. This is one of three
           proteins of the type I secretion apparatus. Targeted
           proteins are not cleaved at the N-terminus, but rather
           carry signals located toward the extreme C-terminus to
           direct type I secretion.
          Length = 694

 Score = 28.2 bits (63), Expect = 2.2
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 63  PSRVVILVGPSGSGKSCLA 81
           P   + +VGPSGSGKS L 
Sbjct: 482 PGEFIGIVGPSGSGKSTLT 500


>gnl|CDD|131817 TIGR02770, nickel_nikD, nickel import ATP-binding protein NikD.
           This family represents the NikD subunit of a
           multisubunit nickel import ABC transporter complex.
           Nickel, once imported, may be used in urease and in
           certain classes of hydrogenase and superoxide dismutase.
           NikD and NikE are homologous.
          Length = 230

 Score = 28.1 bits (63), Expect = 2.3
 Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 16/57 (28%)

Query: 65  RVVILVGPSGSGKS--CLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLL 119
            V+ LVG SGSGKS  CLA              I   L   L  T   +LL+   LL
Sbjct: 13  EVLALVGESGSGKSLTCLA--------------ILGLLPPGLTQTSGEILLDGRPLL 55


>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
          protein; Provisional.
          Length = 369

 Score = 28.1 bits (63), Expect = 2.3
 Identities = 10/14 (71%), Positives = 11/14 (78%)

Query: 67 VILVGPSGSGKSCL 80
          V+ VGPSG GKS L
Sbjct: 32 VVFVGPSGCGKSTL 45


>gnl|CDD|181651 PRK09105, PRK09105, putative aminotransferase; Provisional.
          Length = 370

 Score = 28.1 bits (63), Expect = 2.4
 Identities = 8/14 (57%), Positives = 10/14 (71%)

Query: 58  SWPSWPSRVVILVG 71
           SWP WP+ V + VG
Sbjct: 339 SWPIWPNWVRVTVG 352


>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
          Length = 413

 Score = 27.7 bits (63), Expect = 2.4
 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 12/36 (33%)

Query: 67  VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDS 102
           +IL GP G+GK+ LA I            IA + D+
Sbjct: 39  MILWGPPGTGKTTLARI------------IAGATDA 62


>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter.  This
           model describes ABC-type bacteriocin transporter. The
           amino terminal domain (pfam03412) processes the
           N-terminal leader peptide from the bacteriocin while
           C-terminal domains resemble ABC transporter membrane
           protein and ATP-binding cassette domain. In general,
           bacteriocins are agents which are responsible for
           killing or inhibiting the closely related species or
           even different strains of the same species. Bacteriocins
           are usually encoded by bacterial plasmids. Bacteriocins
           are named after the species and hence in literature one
           encounters various names e.g., leucocin from Leuconostic
           geldium; pedicocin from Pedicoccus acidilactici; sakacin
           from Lactobacillus sake etc.
          Length = 708

 Score = 27.8 bits (62), Expect = 2.5
 Identities = 20/70 (28%), Positives = 24/70 (34%), Gaps = 16/70 (22%)

Query: 66  VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQ 125
              +VG SGSGKS L                AK L          +LL    L D +   
Sbjct: 502 KTTIVGMSGSGKSTL----------------AKLLVGFFQARSGEILLNGFSLKDIDRHT 545

Query: 126 LFHIINSIHQ 135
           L   IN + Q
Sbjct: 546 LRQFINYLPQ 555


>gnl|CDD|184592 PRK14254, PRK14254, phosphate ABC transporter ATP-binding
          protein; Provisional.
          Length = 285

 Score = 27.8 bits (62), Expect = 2.5
 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 38 ISRDDLLVHSAIEQAVRLID-SWPSWPSRVVILVGPSGSGKS 78
          I   DL V    EQA+  +    P   ++V  ++GPSG GKS
Sbjct: 40 IEARDLNVFYGDEQALDDVSMDIPE--NQVTAMIGPSGCGKS 79


>gnl|CDD|184594 PRK14264, PRK14264, phosphate ABC transporter ATP-binding protein;
           Provisional.
          Length = 305

 Score = 27.9 bits (62), Expect = 2.5
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 6/59 (10%)

Query: 38  ISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKS----CLANIWSDKSRSTR 92
           +S +DL V+   + A++ + S       V  L+GPSG GKS    CL N  +D+ ++ R
Sbjct: 46  LSVEDLDVYYGDDHALKGV-SMDIPEKSVTALIGPSGCGKSTFLRCL-NRMNDRIKAAR 102


>gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase.  Members of this family
           are the enzyme guanylate kinase, also called GMP kinase.
           This enzyme transfers a phosphate from ATP to GMP,
           yielding ADP and GDP.
          Length = 180

 Score = 27.8 bits (63), Expect = 2.5
 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 8/47 (17%)

Query: 64  SRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110
             ++++ GPSG GKS L     ++  + +F        SI   TRKP
Sbjct: 1   GLLIVISGPSGVGKSTLVKALLEEDPNLKF--------SISATTRKP 39


>gnl|CDD|172578 PRK14088, dnaA, chromosomal replication initiation protein;
           Provisional.
          Length = 440

 Score = 27.9 bits (62), Expect = 2.5
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 111 VLLEDIDLL---DFNDTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATV 167
           +L++D+  L       T+LFH  N +H     +++ +   P         L SR +   V
Sbjct: 198 LLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLV 257

Query: 168 VKISLPDDDFLEKVIVKM 185
            K+  PD++  +K+  KM
Sbjct: 258 AKLEPPDEETRKKIARKM 275


>gnl|CDD|182980 PRK11124, artP, arginine transporter ATP-binding subunit;
          Provisional.
          Length = 242

 Score = 27.7 bits (62), Expect = 2.7
 Identities = 9/15 (60%), Positives = 13/15 (86%)

Query: 66 VVILVGPSGSGKSCL 80
           ++L+GPSG+GKS L
Sbjct: 30 TLVLLGPSGAGKSSL 44


>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
          Provisional.
          Length = 353

 Score = 27.7 bits (62), Expect = 2.7
 Identities = 11/17 (64%), Positives = 13/17 (76%)

Query: 67 VILVGPSGSGKSCLANI 83
          V L+GPSGSGK+ L  I
Sbjct: 31 VALLGPSGSGKTTLLRI 47


>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
          Length = 259

 Score = 27.7 bits (62), Expect = 2.8
 Identities = 9/15 (60%), Positives = 13/15 (86%)

Query: 67  VILVGPSGSGKSCLA 81
           ++L+GPSG GK+ LA
Sbjct: 105 IVLLGPSGVGKTHLA 119


>gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein;
           Provisional.
          Length = 623

 Score = 27.9 bits (62), Expect = 2.8
 Identities = 12/21 (57%), Positives = 14/21 (66%)

Query: 58  SWPSWPSRVVILVGPSGSGKS 78
           S+  WP   + LVG SGSGKS
Sbjct: 344 SFDLWPGETLSLVGESGSGKS 364


>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
           Provisional.
          Length = 588

 Score = 27.6 bits (62), Expect = 3.0
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 63  PSRVVILVGPSGSGKSCLANI 83
           P + V +VGP+G+GKS L N+
Sbjct: 360 PGQTVAIVGPTGAGKSTLINL 380


>gnl|CDD|178685 PLN03140, PLN03140, ABC transporter G family member; Provisional.
          Length = 1470

 Score = 27.5 bits (61), Expect = 3.1
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 63  PSRVVILVGPSGSGKSCL 80
           PSR+ +L+GP  SGK+ L
Sbjct: 190 PSRMTLLLGPPSSGKTTL 207


>gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
           HflB(FtsH) is a pleiotropic protein required for correct
           cell division in bacteria. It has ATP-dependent zinc
           metalloprotease activity. It was formerly designated
           cell division protein FtsH.
          Length = 495

 Score = 27.6 bits (62), Expect = 3.2
 Identities = 10/15 (66%), Positives = 13/15 (86%)

Query: 67  VILVGPSGSGKSCLA 81
           V+LVGP G+GK+ LA
Sbjct: 91  VLLVGPPGTGKTLLA 105


>gnl|CDD|150194 pfam09439, SRPRB, Signal recognition particle receptor beta
           subunit.  The beta subunit of the signal recognition
           particle receptor (SRP) is a transmembrane GTPase which
           anchors the alpha subunit to the endoplasmic reticulum
           membrane.
          Length = 181

 Score = 27.4 bits (61), Expect = 3.2
 Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 64  SRVVILVGPSGSGKSCLAN-IWSDKSRSTRFSNIAKSLDSILIDTRKPVLLED 115
              VI+ G   SGK+ L   + +   R T  S    +    + +    + L D
Sbjct: 3   QPAVIIAGLCDSGKTSLFTLLTTGSVRKTVTSQEPSAAYKYMNNKGNSLTLID 55


>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
           Provisional.
          Length = 388

 Score = 27.6 bits (61), Expect = 3.4
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 65  RVVILVGPSGSGKSC----LANIWSDKSRSTRFSNIAKSLDSILIDTRKPV 111
           RV ILVGP+G GK+     LA I+   S     +    ++D+  I  +K +
Sbjct: 175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQI 225


>gnl|CDD|182569 PRK10584, PRK10584, putative ABC transporter ATP-binding protein
          YbbA; Provisional.
          Length = 228

 Score = 27.4 bits (61), Expect = 3.4
 Identities = 10/21 (47%), Positives = 12/21 (57%)

Query: 63 PSRVVILVGPSGSGKSCLANI 83
              + L+G SGSGKS L  I
Sbjct: 35 RGETIALIGESGSGKSTLLAI 55


>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. 
          Length = 282

 Score = 27.3 bits (61), Expect = 3.5
 Identities = 8/13 (61%), Positives = 10/13 (76%)

Query: 65  RVVILVGPSGSGK 77
            V+ LVGP+G GK
Sbjct: 195 GVIALVGPTGVGK 207


>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK).  Important
          residue (active site in E.coli) is residue 100 of the
          seed alignment.
          Length = 184

 Score = 27.4 bits (61), Expect = 3.5
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 64 SRVVILVGPSGSGKSCLAN 82
            V+ L G SGSGKS +AN
Sbjct: 18 GVVIWLTGLSGSGKSTIAN 36


>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
           Provisional.
          Length = 445

 Score = 27.5 bits (61), Expect = 3.6
 Identities = 33/204 (16%), Positives = 79/204 (38%), Gaps = 40/204 (19%)

Query: 30  FSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCL--------- 80
            +F   L ++ ++ L H  +++  ++ +    +P   + L GP GSGK+ L         
Sbjct: 108 MTFANFL-VTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALR 166

Query: 81  ----------ANIWSDKSRS-------TRFSNIAKSLDSILIDTRKPVLLEDIDLLD--- 120
                     + ++++   S        RF    +++D++ I+        DI++     
Sbjct: 167 ESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIE--------DIEVFSGKG 218

Query: 121 FNDTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKIS-LPDDDFLE 179
               + FH  NS+H     +++++   P         L SR +    + +  L  +  L 
Sbjct: 219 ATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEG-LR 277

Query: 180 KVIVKMFADRQIFIDKKLAAYIVQ 203
             + +      I I++    ++++
Sbjct: 278 SFLERKAEALSIRIEETALDFLIE 301


>gnl|CDD|184193 PRK13633, PRK13633, cobalt transporter ATP-binding subunit;
           Provisional.
          Length = 280

 Score = 27.4 bits (61), Expect = 3.6
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 17/59 (28%)

Query: 66  VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDT 124
           +VIL G +GSGKS                 IAK ++++LI +   V ++ +D  D  + 
Sbjct: 39  LVIL-GRNGSGKS----------------TIAKHMNALLIPSEGKVYVDGLDTSDEENL 80


>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding
          protein. 
          Length = 237

 Score = 27.5 bits (61), Expect = 3.7
 Identities = 11/15 (73%), Positives = 13/15 (86%)

Query: 66 VVILVGPSGSGKSCL 80
          +V L+GPSGSGKS L
Sbjct: 28 LVALLGPSGSGKSTL 42


>gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein;
          Provisional.
          Length = 272

 Score = 27.3 bits (61), Expect = 3.8
 Identities = 10/16 (62%), Positives = 11/16 (68%)

Query: 65 RVVILVGPSGSGKSCL 80
          RV   +GPSG GKS L
Sbjct: 52 RVTAFIGPSGCGKSTL 67


>gnl|CDD|130045 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
          protein.  This model represents the ATP-binding protein
          of a family of ABC transporters for inorganic
          phosphate. In the model species Escherichia coli, a
          constitutive transporter for inorganic phosphate, with
          low affinity, is also present. The high affinity
          transporter that includes this polypeptide is induced
          when extracellular phosphate concentrations are low.
          The proteins most similar to the members of this family
          but not included appear to be amino acid transporters.
          Length = 247

 Score = 27.3 bits (61), Expect = 3.9
 Identities = 10/15 (66%), Positives = 11/15 (73%)

Query: 66 VVILVGPSGSGKSCL 80
          V  L+GPSG GKS L
Sbjct: 29 VTALIGPSGCGKSTL 43


>gnl|CDD|161743 TIGR00174, miaA, tRNA isopentenyltransferase (miaA).  Catalyzes the
           first step in the modification of an adenosine near the
           anticodon to 2-methylthio-N6-isopentyladenosine.
          Length = 287

 Score = 27.4 bits (61), Expect = 3.9
 Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 32/94 (34%)

Query: 66  VVILVGPSGSGKSCL---------ANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLED- 115
           V+ ++GP+  GKS L         A I S  S       I K +D   I T KP L E  
Sbjct: 1   VIFIMGPTAVGKSQLAIQLAKKLNAEIISVDSMQ-----IYKGMD---IGTAKPSLQERE 52

Query: 116 ------IDLLDFND--------TQLFHIINSIHQ 135
                 ID+LD ++        T   + I  I  
Sbjct: 53  GIPHHLIDILDPSESYSAADFQTLALNAIADITA 86


>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal.  Members
           of this protein are L-seryl-tRNA(Sec) kinase. This
           enzyme is part of a two-step pathway in Eukaryota and
           Archaea for performing selenocysteine biosynthesis by
           changing serine misacylated on selenocysteine-tRNA to
           selenocysteine. This enzyme performs the first step,
           phosphorylation of the OH group of the serine side
           chain. This family represents archaeal proteins with
           this activity.
          Length = 249

 Score = 27.1 bits (60), Expect = 3.9
 Identities = 11/38 (28%), Positives = 15/38 (39%)

Query: 66  VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSI 103
           ++IL G  G GKS  +   + K        I    D I
Sbjct: 1   LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLI 38


>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
           utilisation.  Members of this family function in
           ethanolamine and propanediol degradation pathways,
           however the exact roles of these proteins is poorly
           understood.
          Length = 143

 Score = 27.2 bits (61), Expect = 4.0
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 13/47 (27%)

Query: 67  VILVGPSGSGKSCLA------NIWSDKSRSTRFSNIAKSLDSILIDT 107
           ++L+G SG GK+ L        +   K+++  FS+         IDT
Sbjct: 4   IMLIGRSGCGKTTLTQALNGEELKYKKTQAIEFSDNM-------IDT 43


>gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
           (clpX).  A member of the ATP-dependent proteases, ClpX
           has ATP-dependent chaperone activity and is required for
           specific ATP-dependent proteolytic activities expressed
           by ClpPX. The gene is also found to be involved in
           stress tolerance in Bacillus subtilis and is essential
           for the efficient acquisition of genes specifying type
           IA and IB restriction.
          Length = 413

 Score = 27.0 bits (60), Expect = 4.2
 Identities = 9/15 (60%), Positives = 14/15 (93%)

Query: 67  VILVGPSGSGKSCLA 81
           ++L+GP+GSGK+ LA
Sbjct: 119 ILLIGPTGSGKTLLA 133


>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
          protein.  Phosphonates are a class of
          phosphorus-containing organic compound with a stable
          direct C-P bond rather than a C-O-P linkage. A number
          of bacterial species have operons, typically about 14
          genes in size, with genes for ATP-dependent transport
          of phosphonates, degradation, and regulation of the
          expression of the system. Members of this protein
          family are the ATP-binding cassette component of
          tripartite ABC transporters of phosphonates.
          Length = 243

 Score = 27.3 bits (61), Expect = 4.2
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 63 PSRVVILVGPSGSGKSCL 80
          P   V ++GPSG+GKS L
Sbjct: 27 PGEFVAIIGPSGAGKSTL 44


>gnl|CDD|184583 PRK14237, PRK14237, phosphate transporter ATP-binding protein;
          Provisional.
          Length = 267

 Score = 27.0 bits (60), Expect = 4.3
 Identities = 16/44 (36%), Positives = 28/44 (63%), Gaps = 3/44 (6%)

Query: 36 LGISRDDLLVHSAIEQAVRLID-SWPSWPSRVVILVGPSGSGKS 78
          + +S  DL V+   ++A++ ID  +    +++  L+GPSGSGKS
Sbjct: 19 IALSTKDLHVYYGKKEAIKGIDMQFEK--NKITALIGPSGSGKS 60


>gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
          Length = 248

 Score = 27.2 bits (61), Expect = 4.3
 Identities = 9/15 (60%), Positives = 13/15 (86%)

Query: 66 VVILVGPSGSGKSCL 80
          ++ LVGP+G+GKS L
Sbjct: 24 ILHLVGPNGAGKSTL 38


>gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain.  This is a family of PrkA
          bacterial and archaeal serine kinases approximately 630
          residues long. This is the N-terminal AAA domain.
          Length = 361

 Score = 27.3 bits (61), Expect = 4.4
 Identities = 8/17 (47%), Positives = 12/17 (70%)

Query: 65 RVVILVGPSGSGKSCLA 81
          +++ L+GP G GKS L 
Sbjct: 79 QILYLLGPVGGGKSSLV 95


>gnl|CDD|172749 PRK14261, PRK14261, phosphate ABC transporter ATP-binding
          protein; Provisional.
          Length = 253

 Score = 27.1 bits (60), Expect = 4.4
 Identities = 11/16 (68%), Positives = 12/16 (75%)

Query: 65 RVVILVGPSGSGKSCL 80
          RV  L+GPSG GKS L
Sbjct: 33 RVTALIGPSGCGKSTL 48


>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
          domain fusion protein; Reviewed.
          Length = 725

 Score = 26.9 bits (60), Expect = 4.6
 Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 1/29 (3%)

Query: 68 ILVGPSGSGKSCLANIWSDKSRSTRFSNI 96
          IL GP G GK+ LA I ++ +R+  FS++
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRA-HFSSL 83


>gnl|CDD|178576 PLN02997, PLN02997, flavonol synthase.
          Length = 325

 Score = 26.9 bits (59), Expect = 4.7
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 9/47 (19%)

Query: 155 LPDLCSRLKAAT---------VVKISLPDDDFLEKVIVKMFADRQIF 192
           LP L  +L ++T         VV +S+ D+DFL + +VK   +  +F
Sbjct: 14  LPSLSKQLASSTLGGSAVDVPVVDLSVSDEDFLVREVVKASEEWGVF 60


>gnl|CDD|183056 PRK11248, tauB, taurine transporter ATP-binding subunit;
          Provisional.
          Length = 255

 Score = 27.0 bits (60), Expect = 4.7
 Identities = 8/21 (38%), Positives = 15/21 (71%)

Query: 63 PSRVVILVGPSGSGKSCLANI 83
             +++++GPSG GK+ L N+
Sbjct: 26 SGELLVVLGPSGCGKTTLLNL 46


>gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed.
          Length = 251

 Score = 27.0 bits (60), Expect = 4.9
 Identities = 9/18 (50%), Positives = 15/18 (83%)

Query: 63 PSRVVILVGPSGSGKSCL 80
          P +++ L+GP+G+GKS L
Sbjct: 29 PGKILTLLGPNGAGKSTL 46


>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
          Length = 328

 Score = 27.0 bits (61), Expect = 5.0
 Identities = 11/17 (64%), Positives = 13/17 (76%)

Query: 67 VILVGPSGSGKSCLANI 83
          V+L GP G GK+ LANI
Sbjct: 54 VLLYGPPGLGKTTLANI 70


>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily.  This
           subfamily of the AAA family ATPases includes two members
           each from three archaeal species. It also includes yeast
           CDC48 (cell division control protein 48) and the human
           ortholog, transitional endoplasmic reticulum ATPase
           (valosin-containing protein). These proteins in
           eukaryotes are involved in the budding and transfer of
           membrane from the transitional endoplasmic reticulum to
           the Golgi apparatus.
          Length = 733

 Score = 26.8 bits (59), Expect = 5.0
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 63  PSRVVILVGPSGSGKSCLA 81
           P + V+L GP G+GK+ LA
Sbjct: 211 PPKGVLLYGPPGTGKTLLA 229



 Score = 26.8 bits (59), Expect = 5.7
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 11/51 (21%)

Query: 49  IEQAVRLIDSWP-----------SWPSRVVILVGPSGSGKSCLANIWSDKS 88
           ++Q +R    WP             P + V+L GP G+GK+ LA   + +S
Sbjct: 461 VKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATES 511


>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
           protein; Provisional.
          Length = 438

 Score = 27.0 bits (60), Expect = 5.1
 Identities = 12/29 (41%), Positives = 20/29 (68%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRST 91
           P + VIL GP G+GK+ LA   ++++ +T
Sbjct: 216 PPKGVILYGPPGTGKTLLAKAVANETSAT 244


>gnl|CDD|184131 PRK13546, PRK13546, teichoic acids export protein ATP-binding
          subunit; Provisional.
          Length = 264

 Score = 26.7 bits (59), Expect = 5.2
 Identities = 12/18 (66%), Positives = 15/18 (83%)

Query: 66 VVILVGPSGSGKSCLANI 83
          V+ LVG +GSGKS L+NI
Sbjct: 52 VIGLVGINGSGKSTLSNI 69


>gnl|CDD|180683 PRK06762, PRK06762, hypothetical protein; Provisional.
          Length = 166

 Score = 26.9 bits (60), Expect = 5.3
 Identities = 8/20 (40%), Positives = 14/20 (70%)

Query: 63 PSRVVILVGPSGSGKSCLAN 82
           + ++I+ G SGSGK+ +A 
Sbjct: 1  MTTLIIIRGNSGSGKTTIAK 20


>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
           Provisional.
          Length = 255

 Score = 26.9 bits (60), Expect = 5.5
 Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 16/64 (25%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122
             ++  L+GP+G GKS L                 K    +L      V L D  +   +
Sbjct: 27  TGKITALIGPNGCGKSTL----------------LKCFARLLTPQSGTVFLGDKPISMLS 70

Query: 123 DTQL 126
             QL
Sbjct: 71  SRQL 74


>gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional.
          Length = 327

 Score = 26.9 bits (60), Expect = 5.6
 Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)

Query: 63 PSRVVIL--VGPSGSGKSCLAN 82
          P R V+L   G SG GK+    
Sbjct: 5  PDRPVLLGVAGDSGCGKTTFLR 26


>gnl|CDD|152038 pfam11602, NTPase_P4, ATPase P4 of dsRNA bacteriophage phi-12.  P4
           is a packaging motor which is involved in the packaging
           of phi-12 genome into preformed capsids using ATP. P4 is
           located at the vertices of the icosahedral capsid. ATP
           drives RNA translocation through cooperative
           conformational changes.
          Length = 320

 Score = 26.9 bits (59), Expect = 5.7
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 12/72 (16%)

Query: 62  WPSR-----VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLD----SILIDTRKPVL 112
           W S      +VI+ G +GSGKS   N   D   + R+    +  D    ++ +D    +L
Sbjct: 104 WASEGIYSGMVIVTGKTGSGKSEALNG-KDPDVTIRWGEPLEGYDTLDFNVFVDDLAEML 162

Query: 113 LEDIDL--LDFN 122
           +  I L  L   
Sbjct: 163 IVCIGLAMLQHR 174


>gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter
          subunit; Provisional.
          Length = 262

 Score = 26.5 bits (58), Expect = 5.7
 Identities = 11/15 (73%), Positives = 13/15 (86%)

Query: 66 VVILVGPSGSGKSCL 80
          +V L+GPSGSGKS L
Sbjct: 32 MVALLGPSGSGKSTL 46


>gnl|CDD|182707 PRK10762, PRK10762, D-ribose transporter ATP binding protein;
          Provisional.
          Length = 501

 Score = 26.5 bits (59), Expect = 5.9
 Identities = 10/19 (52%), Positives = 15/19 (78%)

Query: 62 WPSRVVILVGPSGSGKSCL 80
          +P RV+ LVG +G+GKS +
Sbjct: 28 YPGRVMALVGENGAGKSTM 46


>gnl|CDD|184126 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
          Provisional.
          Length = 207

 Score = 26.8 bits (60), Expect = 6.0
 Identities = 8/14 (57%), Positives = 12/14 (85%)

Query: 67 VILVGPSGSGKSCL 80
          ++L GP+GSGK+ L
Sbjct: 31 LVLTGPNGSGKTTL 44


>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
          Provisional.
          Length = 260

 Score = 26.5 bits (59), Expect = 6.1
 Identities = 9/16 (56%), Positives = 11/16 (68%)

Query: 65 RVVILVGPSGSGKSCL 80
          +V   +GPSG GKS L
Sbjct: 40 QVTAFIGPSGCGKSTL 55


>gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain.  This is a family of PrkA
           bacterial and archaeal serine kinases approximately 630
           residues long. This is the N-terminal AAA domain.
          Length = 358

 Score = 26.7 bits (59), Expect = 6.1
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 65  RVVILVGPSGSGKSCLA 81
           +++ L+GP G GKS LA
Sbjct: 86  QILYLLGPVGGGKSSLA 102


>gnl|CDD|128968 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM.
           This superfamily contains MoaA, NifB, PqqE,
           coproporphyrinogen III oxidase, biotin synthase and MiaB
           families, and includes a representative in the
           eukaryotic elongator subunit, Elp-3. Some members of the
           family are methyltransferases.
          Length = 216

 Score = 26.6 bits (59), Expect = 6.3
 Identities = 21/112 (18%), Positives = 40/112 (35%), Gaps = 9/112 (8%)

Query: 79  CLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDT-----QLFHIINSI 133
           C       K RS     + + ++ +     K +L+  + +     T     QL  ++ +I
Sbjct: 18  CSFPSARGKLRSRYLEALVREIELLAEKGEKEILVGTVFIGGGTPTLLSPEQLEELLEAI 77

Query: 134 HQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKISLP----DDDFLEKV 181
            +          T     G    +L   LK A V ++SL      D+ L+ +
Sbjct: 78  REILGLADDVEITIETRPGTLTEELLEALKEAGVNRVSLGVQSGSDEVLKAI 129


>gnl|CDD|163576 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
          PQQ-dependent alcohol dehydrogenase system.  Members of
          this protein family are the ATP-binding subunit of an
          ABC transporter system that is associated with PQQ
          biosynthesis and PQQ-dependent alcohol dehydrogenases.
          While this family shows homology to several efflux ABC
          transporter subunits, the presence of a periplasmic
          substrate-binding protein and association with systems
          for catabolism of alcohols suggests a role in import
          rather than detoxification.
          Length = 236

 Score = 26.5 bits (59), Expect = 6.4
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 63 PSRVVILVGPSGSGKSCL 80
          P   V L+GP+G+GKS L
Sbjct: 26 PGEFVALLGPNGAGKSTL 43


>gnl|CDD|130344 TIGR01277, thiQ, thiamine ABC transporter, ATP-binding protein.
          This model describes the energy-transducing ATPase
          subunit ThiQ of the ThiBPQ thiamine (and thiamine
          pyrophosphate) ABC transporter in several
          Proteobacteria. This protein is found so far only in
          Proteobacteria, and is found in complete genomes only
          if the ThiB and ThiP subunits are also found.
          Length = 213

 Score = 26.4 bits (58), Expect = 6.4
 Identities = 10/17 (58%), Positives = 14/17 (82%)

Query: 67 VILVGPSGSGKSCLANI 83
          V ++GPSG+GKS L N+
Sbjct: 27 VAIMGPSGAGKSTLLNL 43


>gnl|CDD|162629 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA.  This model
           represents HrpA, one of two related but uncharacterized
           DEAH-box ATP-dependent helicases in many Proteobacteria
           and a few high-GC Gram-positive bacteria. HrpA is about
           1300 amino acids long, while its paralog HrpB, also
           uncharacterized, is about 800 amino acids long. Related
           characterized eukarotic proteins are RNA helicases
           associated with pre-mRNA processing.
          Length = 1283

 Score = 26.7 bits (59), Expect = 6.6
 Identities = 13/41 (31%), Positives = 22/41 (53%)

Query: 108 RKPVLLEDIDLLDFNDTQLFHIINSIHQYDSSLLMTARTFP 148
           R+ +L+++  L DF D +L   IN+   +DS     +R  P
Sbjct: 771 RRDILVDEQTLFDFYDGRLPEDINNARHFDSWWKKASRKQP 811


>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding
          protein; Provisional.
          Length = 249

 Score = 26.3 bits (58), Expect = 6.7
 Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)

Query: 63 PSR-VVILVGPSGSGKSCL 80
          P+R V  L+GPSG GKS L
Sbjct: 27 PARQVTALIGPSGCGKSTL 45


>gnl|CDD|149124 pfam07880, T4_gp9_10, Bacteriophage T4 gp9/10-like protein.  The
           members of this family are similar to gene products 9
           (gp9) and 10 (gp10) of bacteriophage T4. Both proteins
           are components of the viral baseplate. Gp9 connects the
           long tail fibres of the virus to the baseplate and
           triggers tail contraction after viral attachment to a
           host cell. The protein is active as a trimer, with each
           monomer being composed of three domains. The N-terminal
           domain consists of an extended polypeptide chain and two
           alpha helices. The alpha1 helix from each of the three
           monomers in the trimer interacts with its counterparts
           to form a coiled-coil structure. The middle domain is a
           seven-stranded beta-sandwich that is thought to be a
           novel protein fold. The C-terminal domain is thought to
           be essential for gp9 trimerisation and is organized into
           an eight- stranded antiparallel beta-barrel, which was
           found to resemble the 'jelly roll' fold found in many
           viral capsid proteins. The long flexible region between
           the N-terminal and middle domains may be required for
           the function of gp9 to transmit signals from the long
           tail fibres. Together with gp11, gp10 initiates the
           assembly of wedges that then go on to associate with a
           hub to form the viral baseplate.
          Length = 272

 Score = 26.6 bits (59), Expect = 6.9
 Identities = 19/71 (26%), Positives = 25/71 (35%), Gaps = 12/71 (16%)

Query: 53  VRLIDSWPSW-PSRVVILVGPSG---SGKSCLANIWSDKSR--------STRFSNIAKSL 100
           +  I+S  SW  +  V +V  SG    G S    I    S             S    S+
Sbjct: 102 IEFINSNGSWSVTNPVTIVPQSGDTIKGSSGNLEITKPYSDVELVCCSPGGSVSRWEYSI 161

Query: 101 DSILIDTRKPV 111
           +SI  D   PV
Sbjct: 162 ESIFGDDLSPV 172


>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
          Length = 167

 Score = 26.5 bits (59), Expect = 7.0
 Identities = 10/15 (66%), Positives = 12/15 (80%)

Query: 67 VILVGPSGSGKSCLA 81
          +IL+G  GSGKS LA
Sbjct: 4  IILIGSGGSGKSTLA 18


>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
          This model describes the ATP binding subunit of the
          multisubunit cobalt transporter in bacteria and its
          equivalents in archaea. The model is restricted to ATP
          subunit that is a part of the cobalt transporter, which
          belongs to the ABC transporter superfamily (ATP Binding
          Cassette). The model excludes ATP binding subunit that
          are associated with other transporters belonging to ABC
          transporter superfamily. This superfamily includes two
          groups, one which catalyze the uptake of small
          molecules, including ions from the external milieu and
          the other group which is engaged in the efflux of small
          molecular weight compounds and ions from within the
          cell. Energy derived from the hydrolysis of ATP drive
          the both the process of uptake and efflux.
          Length = 190

 Score = 26.2 bits (58), Expect = 7.1
 Identities = 8/17 (47%), Positives = 12/17 (70%)

Query: 64 SRVVILVGPSGSGKSCL 80
            V+ L+G +G+GKS L
Sbjct: 18 GEVLALLGANGAGKSTL 34


>gnl|CDD|180254 PRK05782, PRK05782, bifunctional sirohydrochlorin cobalt
           chelatase/precorrin-8X methylmutase; Validated.
          Length = 335

 Score = 26.3 bits (58), Expect = 7.2
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 10/76 (13%)

Query: 162 LKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKL-AAYIVQRMERSLVFAEKLVDKMD 220
           L+ A  VKIS   +D L+  I  + A+ +I  D K+ +A I  R ++       ++D   
Sbjct: 182 LELAKYVKIS---NDLLDAGIEAIRAESEIVADVKMVSAGI--RWKK----VTCMIDAER 232

Query: 221 NLALSRGMGITRSLAA 236
              L++ +GITR+ AA
Sbjct: 233 TKELAKELGITRAAAA 248


>gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
          Family protein. 
          Length = 617

 Score = 26.2 bits (58), Expect = 7.3
 Identities = 9/27 (33%), Positives = 17/27 (62%)

Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSR 89
          P  ++ ++G SG+GK+ L N  + +S 
Sbjct: 50 PGELLAVMGSSGAGKTTLMNALAFRSP 76


>gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein
          PhnL.  Members of this family are the PhnL protein of
          C-P lyase systems for utilization of phosphonates.
          These systems resemble phosphonatase-based systems in
          having a three component ABC transporter, where
          TIGR01097 is the permease, TIGR01098 is the
          phosphonates binding protein, and TIGR02315 is the
          ATP-binding cassette (ABC) protein. They differ,
          however, in having, typically, ten or more additional
          genes, many of which are believed to form a
          membrane-associated C-P lysase complex. This protein
          (PhnL) and the adjacent-encoded PhnK (TIGR02323)
          resemble transporter ATP-binding proteins but are
          suggested, based on mutatgenesis studies, to be part of
          this C-P lyase complex rather than part of a
          transporter per se.
          Length = 224

 Score = 26.2 bits (58), Expect = 7.3
 Identities = 10/14 (71%), Positives = 11/14 (78%)

Query: 67 VILVGPSGSGKSCL 80
          V L GPSG+GKS L
Sbjct: 37 VALSGPSGAGKSTL 50


>gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed.
          Length = 394

 Score = 26.4 bits (59), Expect = 7.4
 Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 20/57 (35%)

Query: 63  PSRVVILVGPSGSGKSCLA-------------------NIWSDKSRSTRFSNIAKSL 100
           P  V+I  GP G+GK+                      N   D++R   FS IA+ L
Sbjct: 55  PLNVLIY-GPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQL 110


>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
           Provisional.
          Length = 432

 Score = 26.1 bits (57), Expect = 8.1
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 65  RVVILVGPSGSGKS 78
           +VV  VGP+GSGK+
Sbjct: 224 KVVFFVGPTGSGKT 237


>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
          Length = 424

 Score = 26.0 bits (58), Expect = 8.2
 Identities = 9/33 (27%), Positives = 14/33 (42%)

Query: 45  VHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGK 77
           +   +   + +          VV LVGP+G GK
Sbjct: 202 LLELLANMIPVRVEDILKQGGVVALVGPTGVGK 234


>gnl|CDD|184315 PRK13768, PRK13768, GTPase; Provisional.
          Length = 253

 Score = 26.0 bits (58), Expect = 8.3
 Identities = 7/16 (43%), Positives = 11/16 (68%)

Query: 66 VVILVGPSGSGKSCLA 81
          +V  +G +GSGK+ L 
Sbjct: 4  IVFFLGTAGSGKTTLT 19


>gnl|CDD|150662 pfam10014, DUF2257, Uncharacterized protein conserved in bacteria
           (DUF2257).  Members of this family of hypothetical
           bacterial proteins have no known function.
          Length = 196

 Score = 26.0 bits (58), Expect = 8.3
 Identities = 10/28 (35%), Positives = 15/28 (53%)

Query: 112 LLEDIDLLDFNDTQLFHIINSIHQYDSS 139
           LLE  D L  +D +L+H +  I   D +
Sbjct: 157 LLEPGDTLLLDDRRLWHYVTPIKPIDPA 184


>gnl|CDD|179060 PRK00549, PRK00549, competence damage-inducible protein A;
           Provisional.
          Length = 414

 Score = 26.3 bits (59), Expect = 8.4
 Identities = 7/20 (35%), Positives = 14/20 (70%)

Query: 174 DDDFLEKVIVKMFADRQIFI 193
           D+D LE+V+ K+  ++ + I
Sbjct: 255 DEDSLEEVVAKLLKEKGLTI 274


>gnl|CDD|172735 PRK14247, PRK14247, phosphate ABC transporter ATP-binding
          protein; Provisional.
          Length = 250

 Score = 26.0 bits (57), Expect = 8.7
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 63 PSRVVILVGPSGSGKSCL 80
           + +  L+GPSGSGKS L
Sbjct: 28 DNTITALMGPSGSGKSTL 45


>gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed.
          Length = 361

 Score = 25.9 bits (58), Expect = 9.0
 Identities = 7/14 (50%), Positives = 9/14 (64%)

Query: 64 SRVVILVGPSGSGK 77
            V +LVG +G GK
Sbjct: 23 PGVNVLVGENGQGK 36


>gnl|CDD|172730 PRK14242, PRK14242, phosphate transporter ATP-binding protein;
          Provisional.
          Length = 253

 Score = 25.9 bits (57), Expect = 9.1
 Identities = 9/14 (64%), Positives = 11/14 (78%)

Query: 65 RVVILVGPSGSGKS 78
          +V  L+GPSG GKS
Sbjct: 33 QVTALIGPSGCGKS 46


>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family.  Many
           proteins may score above the trusted cutoff because an
           internal.
          Length = 364

 Score = 25.9 bits (57), Expect = 9.1
 Identities = 11/29 (37%), Positives = 19/29 (65%)

Query: 63  PSRVVILVGPSGSGKSCLANIWSDKSRST 91
           P + V+L GP G+GK+ LA   + ++ +T
Sbjct: 155 PPKGVLLYGPPGTGKTLLAKAVAHETNAT 183


>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
          Length = 637

 Score = 26.1 bits (58), Expect = 9.3
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 65 RVVILVGPSGSGKSCLA 81
          R V+++G  G+GKS LA
Sbjct: 51 RHVMMIGSPGTGKSMLA 67


>gnl|CDD|132050 TIGR03005, ectoine_ehuA, ectoine/hydroxyectoine ABC transporter,
          ATP-binding protein.  Members of this family are the
          ATP-binding protein of a conserved four gene ABC
          transporter operon found next to ectoine unilization
          operons and ectoine biosynthesis operons. Ectoine is a
          compatible solute that protects enzymes from high
          osmolarity. It is released by some species in response
          to hypoosmotic shock, and it is taken up by a number of
          bacteria as a compatible solute or for consumption.
          This family shows strong sequence similiarity to a
          number of amino acid ABC transporter ATP-binding
          proteins.
          Length = 252

 Score = 25.9 bits (57), Expect = 9.5
 Identities = 11/21 (52%), Positives = 13/21 (61%)

Query: 63 PSRVVILVGPSGSGKSCLANI 83
              V L+GPSGSGKS +  I
Sbjct: 25 AGEKVALIGPSGSGKSTILRI 45


>gnl|CDD|182348 PRK10270, PRK10270, putative aminodeoxychorismate lyase;
           Provisional.
          Length = 340

 Score = 26.0 bits (57), Expect = 9.6
 Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 2/33 (6%)

Query: 147 FPVSW--GVCLPDLCSRLKAATVVKISLPDDDF 177
           FP+    G+ L D   +L+ A  +K +L DD +
Sbjct: 110 FPLRLVEGMRLSDYLKQLREAPYIKHTLSDDKY 142


>gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase.
          Length = 421

 Score = 25.9 bits (57), Expect = 9.8
 Identities = 9/17 (52%), Positives = 15/17 (88%)

Query: 65 RVVILVGPSGSGKSCLA 81
          +V+++ GP+G+GKS LA
Sbjct: 22 KVIVISGPTGAGKSRLA 38


>gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
           The Aquifex aeolicus ortholog is split into consecutive
           open reading frames. Consequently, this model was build
           in fragment mode (-f option).
          Length = 245

 Score = 25.8 bits (57), Expect = 10.0
 Identities = 9/19 (47%), Positives = 12/19 (63%)

Query: 64  SRVVILVGPSGSGKSCLAN 82
           +R+ +  G SG GKS L N
Sbjct: 120 NRISVFAGQSGVGKSSLIN 138


>gnl|CDD|162739 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.
          Length = 1179

 Score = 25.8 bits (57), Expect = 10.0
 Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 3/21 (14%)

Query: 63 PSRVVILVGPSGSGKSCLANI 83
             +  +VGP+G GKS   NI
Sbjct: 22 DKGITGIVGPNGCGKS---NI 39


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.322    0.136    0.401 

Gapped
Lambda     K      H
   0.267   0.0738    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,950,515
Number of extensions: 246237
Number of successful extensions: 959
Number of sequences better than 10.0: 1
Number of HSP's gapped: 949
Number of HSP's successfully gapped: 182
Length of query: 246
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,028,145
Effective search space: 624362475
Effective search space used: 624362475
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.3 bits)