RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780640|ref|YP_003065053.1| hypothetical protein
CLIBASIA_02635 [Candidatus Liberibacter asiaticus str. psy62]
         (110 letters)



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

 Score = 40.9 bits (97), Expect = 7e-05
 Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 32 IEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWL 73
          + ++ FR + E   +E +  + ++ G+NG GK++L EAI  L
Sbjct: 6  LSLTDFRNYEE-LDLELSPGVNVLVGENGQGKTNLLEAIYLL 46


>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
          Length = 895

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 46 IEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGDSIKK 89
          IEF   + I+ G+NG GKSS+ +AI +  +   +  K  D IKK
Sbjct: 19 IEFDTGINIITGKNGAGKSSIVDAIRFALFTDKRTEKIEDMIKK 62


>gnl|CDD|161957 TIGR00611, recf, recF protein.  All proteins in this family for
          which functions are known are DNA binding proteins that
          assist the filamentation of RecA onto DNA for the
          initiation of recombination or recombinational repair.
          This family is based on the phylogenomic analysis of JA
          Eisen (1999, Ph.D. Thesis, Stanford University).
          Length = 365

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGDSI 87
           L  +E++ FR +  +  +E +  + ++ G NG GK++L EAI +L       R H  S 
Sbjct: 2  YLSRLELTDFRNYDAV-DLELSPGVNVIVGPNGQGKTNLLEAIYYL----ALGRSHRTSR 56

Query: 88 KKRSI 92
           K  I
Sbjct: 57 DKPLI 61


>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 32 IEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEW 72
          +E++ F+ F +   I F   +T + G NG GKS++ +AI W
Sbjct: 5  LELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAIRW 45


>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC.  This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 1042

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 28  KLLDIEISHFRGFTEIQKIEFA--DHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGD 85
           K L + + +F  +     I+F     + ++ G+ G GK++L +AI +  YG   RR    
Sbjct: 2   KPLRLTLKNFGSYKGTHTIDFTALGPIFLICGKTGAGKTTLLDAITYALYGKLPRRSEVI 61

Query: 86  SIKKRSIKTPMPMCMA 101
                    P     A
Sbjct: 62  RSLNSLYAAPSEAAFA 77


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGDSI 87
          K+ +++I +FR   +   +EF D + ++ GQNG GKSS+ EAI    Y     +  G  +
Sbjct: 2  KIEELKIKNFRSH-KSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWGHGSKPKG--L 58

Query: 88 KK 89
          KK
Sbjct: 59 KK 60


>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
          Length = 880

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76
          +   + + +F+ + +   +   D +T+++G NG GKSSL EA  +  YG
Sbjct: 2  RFDRVRLENFKCYADAD-LRLEDGVTVIHGVNGSGKSSLLEACFFALYG 49


>gnl|CDD|162740 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.
          Length = 1164

 Score = 33.1 bits (76), Expect = 0.015
 Identities = 17/43 (39%), Positives = 29/43 (67%), Gaps = 2/43 (4%)

Query: 32 IEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLF 74
          IE+ +F+ F + + I F+   T+++G NG GKS++ +AI  LF
Sbjct: 5  IELENFKSFGKKKVIPFSKGFTVISGPNGSGKSNIGDAI--LF 45


>gnl|CDD|161971 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.
          Length = 563

 Score = 31.6 bits (72), Expect = 0.044
 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 29 LLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLF 74
          L ++ I++F     +  +EF   LT++ G+ G GKS + +A+  L 
Sbjct: 2  LTELRINNF-ALIRVLTVEFERGLTVLTGETGAGKSMIIDALSLLG 46


>gnl|CDD|129694 TIGR00606, rad50, rad50.  This family is based on the
          phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
          Stanford University).
          Length = 1311

 Score = 29.6 bits (66), Expect = 0.16
 Identities = 13/35 (37%), Positives = 23/35 (65%)

Query: 42 EIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76
          + Q I+F   LTI+ G NG GK+++ E ++++  G
Sbjct: 20 DKQIIDFFSPLTILVGPNGAGKTTIIECLKYICTG 54


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

 Score = 29.8 bits (68), Expect = 0.16
 Identities = 10/24 (41%), Positives = 16/24 (66%)

Query: 48  FADHLTIVNGQNGYGKSSLSEAIE 71
            A  +T++ GQ+G GKS+L  A+ 
Sbjct: 162 LAGKVTVLAGQSGVGKSTLLNALA 185


>gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional.
          Length = 349

 Score = 29.8 bits (67), Expect = 0.17
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIE 71
          +LL +   ++R       + F   +T V G+N  GK++L EAI 
Sbjct: 2  RLLSLRQLNYRNLA-PPTLAFPPGVTAVVGENAAGKTNLLEAIY 44


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

 Score = 29.6 bits (67), Expect = 0.20
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 10/66 (15%)

Query: 10  CACLSKS-LTSYYARKLI--------FKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNG 60
             CL+K+ L S   ++          ++ L I +    G   + + +  + +T+V G +G
Sbjct: 124 VLCLNKADLVSPTEQQQWQDRLQQWGYQPLFISVETGIGLEALLE-QLRNKITVVAGPSG 182

Query: 61  YGKSSL 66
            GKSSL
Sbjct: 183 VGKSSL 188


>gnl|CDD|183406 PRK12288, PRK12288, GTPase RsgA; Reviewed.
          Length = 347

 Score = 29.0 bits (66), Expect = 0.27
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 23  RKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSL 66
           R + +++L +      G  E++       ++I  GQ+G GKSSL
Sbjct: 179 RNIGYRVLMVSSHTGEGLEELEA-ALTGRISIFVGQSGVGKSSL 221


>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 = 28.1 bits (63), Expect = 0.54
 Identities = 9/24 (37%), Positives = 15/24 (62%)

Query: 47  EFADHLTIVNGQNGYGKSSLSEAI 70
              + +++  GQ+G GKSSL  A+
Sbjct: 117 ALQNRISVFAGQSGVGKSSLINAL 140


>gnl|CDD|150128 pfam09352, DUF1994, Domain of unknown function (DUF1994).  This
           family of proteins are functionally uncharacterized.
          Length = 162

 Score = 27.7 bits (62), Expect = 0.73
 Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 15/85 (17%)

Query: 3   RLRKKNTCACLSKSLTSYYARKLIFKLLDIEISHF-----------RGFTEIQKIEFA-- 49
             +    CA  S +L   Y  K I     ++I H              +T+ Q+  FA  
Sbjct: 48  TFKTGKRCAVASGTLHDPYTGKTITTAAAVDIDHVVPLAEAWDSGASSWTDRQRERFAND 107

Query: 50  -DHLTIVNGQNGYGKSSLSEAIEWL 73
             +L  V+G     K    +  EWL
Sbjct: 108 PANLLAVDGSANRSKGD-KDPAEWL 131


>gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed.
          Length = 1068

 Score = 26.9 bits (60), Expect = 1.1
 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 7/39 (17%)

Query: 60  GYGKSSLSEAIEW-LFYGYTQRRKHGDSIKKRSIKTPMP 97
           G GKS+  EA++W L +    R KH ++IKK +   P P
Sbjct: 172 GVGKSA--EALQWDLSF----RLKHWEAIKKAAESRPAP 204


>gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional.
          Length = 562

 Score = 26.9 bits (60), Expect = 1.2
 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 40 FTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76
            EIQ  +     T++ G+NG GKS++ EA+ +  +G
Sbjct: 19 PIEIQLDKVKK--TLITGKNGAGKSTMLEALTFALFG 53


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

 Score = 26.4 bits (59), Expect = 1.6
 Identities = 7/19 (36%), Positives = 11/19 (57%)

Query: 48 FADHLTIVNGQNGYGKSSL 66
           A    ++ G NG GK++L
Sbjct: 26 AAGEALVLTGPNGSGKTTL 44


>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD
          family.  Members of this protein family have two copies
          of the ABC transporter ATP-binding cassette, but are
          found outside the common ABC transporter operon
          structure that features integral membrane permease
          proteins and substrate-binding proteins encoded next to
          the ATP-binding cassette (ABC domain) protein. The
          member protein ChvD from Agrobacterium tumefaciens was
          identified as both a candidate to interact with VirB8,
          based on yeast two-hybrid analysis, and as an apparent
          regulator of VirG. The general function of this protein
          family is unknown.
          Length = 552

 Score = 26.4 bits (59), Expect = 1.8
 Identities = 21/66 (31%), Positives = 25/66 (37%), Gaps = 25/66 (37%)

Query: 1  MTRLRKKNTCACLSKSLTSYYARKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNG 60
          M R+ K                +K I K  DI +S F G     KI        V G NG
Sbjct: 7  MNRVSK------------VVPPKKEILK--DISLSFFPG----AKIG-------VLGLNG 41

Query: 61 YGKSSL 66
           GKS+L
Sbjct: 42 AGKSTL 47


>gnl|CDD|162972 TIGR02680, TIGR02680, conserved hypothetical protein TIGR02680.
          Members of this protein family belong to a conserved
          gene four-gene neighborhood found sporadically in a
          phylogenetically broad range of bacteria: Nocardia
          farcinica, Symbiobacterium thermophilum, and
          Streptomyces avermitilis (Actinobacteria), Geobacillus
          kaustophilus (Firmicutes), Azoarcus sp. EbN1 and
          Ralstonia solanacearum (Betaproteobacteria). Proteins
          in this family average over 1400 amino acids in length.
          Length = 1353

 Score = 26.3 bits (58), Expect = 2.0
 Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 44 QKIEFADHLTIVNGQNGYGKS-SLSEAIEWLFYGY 77
          Q+  F D   ++ G NG GKS  L   + +L  G 
Sbjct: 18 QEFWFRDGRLLLRGNNGAGKSKVLELLLPFLLDGK 52


>gnl|CDD|182852 PRK10938, PRK10938, putative molybdenum transport ATP-binding
          protein ModF; Provisional.
          Length = 490

 Score = 26.1 bits (58), Expect = 2.1
 Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 7/29 (24%)

Query: 50 DHLTIVNGQ-------NGYGKSSLSEAIE 71
            LT+  G        NG GKS+L+ A+ 
Sbjct: 22 PSLTLNAGDSWAFVGANGSGKSALARALA 50


>gnl|CDD|152563 pfam12128, DUF3584, Protein of unknown function (DUF3584).  This
          protein is found in bacteria and eukaryotes. Proteins
          in this family are typically between 943 to 1234 amino
          acids in length. There are two conserved sequence
          motifs: GKT and YLP.
          Length = 1192

 Score = 25.8 bits (57), Expect = 2.3
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)

Query: 35 SHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76
          SH  G   + +++   H T + G N  GK++L   I  LFYG
Sbjct: 5  SHLPGV--VNELDLDGH-TNICGTNAAGKTTLQRLIP-LFYG 42


>gnl|CDD|163250 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
          protein UrtE.  Members of this protein family are ABC
          transporter ATP-binding subunits associated with urea
          transport and metabolism. This protein is found in a
          conserved five-gene transport operon typically found
          adjacent to urease genes. It was shown in Cyanobacteria
          that disruption leads to the loss of high-affinity urea
          transport activity.
          Length = 230

 Score = 25.6 bits (57), Expect = 2.7
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 13/56 (23%)

Query: 15 KSLTSYYARKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAI 70
           +L  YY +  I + + +E+                 +T V G+NG GK++L + +
Sbjct: 4  SNLNVYYGQSHILRGVSLEVP-------------KGEVTCVLGRNGVGKTTLLKTL 46


>gnl|CDD|162608 TIGR01928, menC_lowGC/arch, o-succinylbenzoic acid (OSB)
           synthetase.  This model describes the enzyme
           o-succinylbenzoic acid synthetase (menC) that is
           involved in one of the steps of the menaquinone
           biosynthesis pathway. It takes SHCHC and makes it into
           2-succinylbenzoate. Included in this model are low GC
           gram positive bacteria and archaea. Also included in the
           seed and in the model are enzymes with the com-name of
           N-acylamino acid racemase (or the more general term,
           racemase / racemase family), which refers to the
           enzyme's industrial application as racemases, and not to
           its biological function as o-succinylbenzoic acid
           synthetase.
          Length = 324

 Score = 25.6 bits (56), Expect = 2.8
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 8/57 (14%)

Query: 1   MTRLRKKN--TCACLSKSLTSYY-ARKLI----FKLLDIEISHFRGFTEIQK-IEFA 49
           M     K   T  CL +S+TS   AR LI     K+++I+     G TE+QK IE  
Sbjct: 214 MLDELAKGTITPICLDESITSLDDARNLIELGNVKVINIKPGRLGGLTEVQKAIETC 270


>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
          Length = 263

 Score = 25.5 bits (56), Expect = 3.1
 Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)

Query: 39  GFTEIQKIEFADHLTIVNG-QNGYGKSSLSEAI 70
           G T+   +E+A     VN    GY ++ ++E+I
Sbjct: 164 GLTKSLAVEYAQSGIRVNAICPGYVRTPMAESI 196


>gnl|CDD|184195 PRK13635, cbiO, cobalt transporter ATP-binding subunit;
          Provisional.
          Length = 279

 Score = 25.4 bits (56), Expect = 3.1
 Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)

Query: 52 LTIVNGQNGYGKSSLSEAIEWLF 74
          + IV G NG GKS+L++ +  L 
Sbjct: 36 VAIV-GHNGSGKSTLAKLLNGLL 57


>gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional.
          Length = 444

 Score = 25.2 bits (55), Expect = 3.6
 Identities = 9/17 (52%), Positives = 14/17 (82%)

Query: 54  IVNGQNGYGKSSLSEAI 70
           ++NGQ+G GK  L++AI
Sbjct: 161 LINGQSGTGKEILAQAI 177


>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 = 25.3 bits (56), Expect = 4.0
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 54 IVNGQNGYGKSSLSEAI 70
           + G NG GKS+LS+ I
Sbjct: 30 AIMGPNGSGKSTLSKTI 46


>gnl|CDD|184717 PRK14508, PRK14508, 4-alpha-glucanotransferase; Provisional.
          Length = 497

 Score = 24.8 bits (55), Expect = 4.8
 Identities = 11/15 (73%), Positives = 11/15 (73%), Gaps = 1/15 (6%)

Query: 27  FKLLDI-EISHFRGF 40
           FKL DI  I HFRGF
Sbjct: 288 FKLYDIVRIDHFRGF 302


>gnl|CDD|162633 TIGR01973, NuoG, NADH-quinone oxidoreductase, chain G.  This model
           represents the G subunit (one of 14: A->N) of the
           NADH-quinone oxidoreductase complex I which generally
           couples NADH and ubiquinone oxidation/reduction in
           bacteria and mammalian mitochondria while translocating
           protons, but may act on NADPH and/or plastoquinone in
           cyanobacteria and plant chloroplasts. This model
           excludes related subunits from formate dehydrogenase
           complexes.
          Length = 603

 Score = 25.0 bits (55), Expect = 4.9
 Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 12/41 (29%)

Query: 74  FYGYTQRRKHGDSIKKRS---------IKTPMPMCMAVPRC 105
            YG  + R      KKR+         IKT M  C+   RC
Sbjct: 113 MYGSDRSRFRE---KKRTVENKYLGPLIKTEMTRCIHCTRC 150


>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
          Length = 234

 Score = 24.9 bits (55), Expect = 5.0
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 52 LTIVNGQNGYGKSSLSEAIEW 72
          L ++ G +G GKS LS+   +
Sbjct: 27 LILIEGDHGTGKSVLSQQFVY 47


>gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.
          This model describes the DndB protein encoded by an
          operon associated with a sulfur-containing modification
          to DNA. The operon is sporadically distributed in
          bacteria, much like some restriction enzyme operons.
          DndD is described as a putative ATPase. The small
          number of examples known so far include species from
          among the Firmicutes, Actinomycetes, Proteobacteria,
          and Cyanobacteria.
          Length = 650

 Score = 24.6 bits (54), Expect = 5.0
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 6/57 (10%)

Query: 25 LIFKLLDIEISHFRGFTEIQKIEFA----DHLTIVNGQNGYGKSSLSEAIEWLFYGY 77
          +I   L +E  +F  +   Q  + +      + ++ G NG GK++L +AI+   YG 
Sbjct: 1  MIILQLTLE--NFGPYRGRQTFDLSPSSPKPIILIGGLNGAGKTTLLDAIQLALYGK 55


>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
           Provisional.
          Length = 638

 Score = 24.6 bits (54), Expect = 5.3
 Identities = 7/17 (41%), Positives = 13/17 (76%)

Query: 54  IVNGQNGYGKSSLSEAI 70
           ++ G+ G GK+ L++AI
Sbjct: 352 LLCGEEGVGKALLAQAI 368


>gnl|CDD|183324 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
          Reviewed.
          Length = 556

 Score = 24.7 bits (55), Expect = 5.6
 Identities = 21/66 (31%), Positives = 25/66 (37%), Gaps = 25/66 (37%)

Query: 1  MTRLRKKNTCACLSKSLTSYYARKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNG 60
          M R+ K                +K I K  DI +S F G     KI        V G NG
Sbjct: 9  MNRVSK------------VVPPKKQILK--DISLSFFPG----AKIG-------VLGLNG 43

Query: 61 YGKSSL 66
           GKS+L
Sbjct: 44 AGKSTL 49


>gnl|CDD|184202 PRK13642, cbiO, cobalt transporter ATP-binding subunit;
          Provisional.
          Length = 277

 Score = 24.7 bits (53), Expect = 5.9
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 57 GQNGYGKSSLSEAIEWLF 74
          GQNG GKS+ +  I+ LF
Sbjct: 40 GQNGSGKSTTARLIDGLF 57


>gnl|CDD|130996 TIGR01941, nqrF, NADH:ubiquinone oxidoreductase,
           Na(+)-translocating, F subunit.  This model represents
           the NqrF subunit of the six-protein, Na(+)-pumping
           NADH-quinone reductase of a number of marine and
           pathogenic Gram-negative bacteria. This oxidoreductase
           complex functions primarily as a sodium ion pump.
          Length = 405

 Score = 24.4 bits (53), Expect = 6.2
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 6   KKNTCACLSKSLTSYYARKLIFKLLDIEISHFR--GFTEIQ----KIEFAD 50
           KK  C  +S    + + ++L+ KL D E   F+  G+ +I+     +++AD
Sbjct: 128 KKWECEVISNDNVATFIKELVLKLPDGESVPFKAGGYIQIEAPPHVVKYAD 178


>gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA;
          Provisional.
          Length = 195

 Score = 24.4 bits (53), Expect = 6.6
 Identities = 10/19 (52%), Positives = 12/19 (63%)

Query: 52 LTIVNGQNGYGKSSLSEAI 70
          +T + G NG GKSSL   I
Sbjct: 28 ITYIKGANGCGKSSLLRMI 46


>gnl|CDD|182970 PRK11111, PRK11111, hypothetical protein; Provisional.
          Length = 214

 Score = 24.1 bits (53), Expect = 7.4
 Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 3/36 (8%)

Query: 6  KKNTCACLSKS---LTSYYARKLIFKLLDIEISHFR 38
          K N  A LS +   L S +    I  L  I I  FR
Sbjct: 44 KTNLTANLSVAIILLISLFLGDFILNLFGISIDSFR 79


>gnl|CDD|150482 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class.  Members
           of this family include various bacterial predicted ABC
           class ATPases.
          Length = 447

 Score = 24.1 bits (53), Expect = 8.6
 Identities = 9/20 (45%), Positives = 15/20 (75%)

Query: 52  LTIVNGQNGYGKSSLSEAIE 71
           +T++ G   +GKS+L EA+E
Sbjct: 245 ITLIVGGGYHGKSTLLEALE 264


  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
   0.324    0.136    0.413 

Gapped
Lambda     K      H
   0.267   0.0771    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,729,884
Number of extensions: 92060
Number of successful extensions: 300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 300
Number of HSP's successfully gapped: 47
Length of query: 110
Length of database: 5,994,473
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,352,265
Effective search space: 147977010
Effective search space used: 147977010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.0 bits)