RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254781225|ref|YP_003065638.1| P4 family phage/plasmid
primase [Candidatus Liberibacter asiaticus str. psy62]
         (789 letters)



>gnl|CDD|33185 COG3378, COG3378, Predicted ATPase [General function prediction
           only].
          Length = 517

 Score =  128 bits (322), Expect = 7e-30
 Identities = 111/472 (23%), Positives = 179/472 (37%), Gaps = 44/472 (9%)

Query: 302 LLASRFSDAYNKAMFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMNFLVS 361
           + A R +D Y   + ++  +G +    D + W K D        L    +  +I      
Sbjct: 42  INAVRLADRYTDKLRAVSAQGTWHV-WDGRRWAKDDA-------LLFLPLDVAIRGLKRQ 93

Query: 362 MKEDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQNVEENSKAKSTAQSLEAGSIFSITSDL 421
                        D +K            Y     E         +   A    + T   
Sbjct: 94  AAIKADHDRGLKADPDKLEAPLSTAGVRSYFPNPTEV--------KEALALVKKAATPKQ 145

Query: 422 LDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEP-------SQEFLDLVS 474
            D     +   +G+LDL TGQ      E   T+     + +           +E+LD V+
Sbjct: 146 QDPDPHLINFANGVLDLRTGQLEPHDPEDRFTRIIPVDYTDPAADPSHCPKWREWLDRVA 205

Query: 475 GYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAE 534
           G     E+ +   R +G +L G    Q+   + G GG+GKST ++LI    G   V +A 
Sbjct: 206 G--GDPELRNLLQRIIGASLTGRVSEQKLFWLYGPGGNGKSTFVDLISNLLGRYNVTSAP 263

Query: 535 ASDIMQNRPPEAGKANPS-LIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNY 593
            +D+      EA   +P  L  L+G R+V +SET +    +  K+K +TGGD ++A    
Sbjct: 264 LTDL------EADDRHPFGLAALVGKRLVTVSETEKGRLDDEGKLKALTGGDVISAERKR 317

Query: 594 GNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTL 653
            + +S +P +       N    +R  D+A WRR +++PF+K     +     KL+ K   
Sbjct: 318 KDFFSFTP-NAKLIQATNHPPRIRGDDEAIWRRLLIVPFEKQFPPAERDD--KLDEKLAA 374

Query: 654 EAK---KWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEE 710
           E      W + G      +GL  D P+  L A EE ++  D    + DD C +GE     
Sbjct: 375 ERPGILNWLVAGFLDLQREGL--DQPQAVLDALEEYKRENDPVFQFCDDECVLGETDGTP 432

Query: 711 SHSLAKS---YSEYREQELNYDRKRISTRTVTLNLK-QKGFIGGIKREKIEK 758
           +         Y  Y+E           ++T        KG   G KR + E 
Sbjct: 433 TAFDNIVLELYEAYQEWCEANGYVVELSKTRFGKELPTKGVPKGRKRHQGET 484


>gnl|CDD|80309 cd04859, Prim_Pol, Prim_Pol: Primase-polymerase (primpol) domain of
           the type found in bifunctional replicases from archaeal
           plasmids, including ORF904 protein of the crenarchaeal
           plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol).
           These primpol domains belong to the archaeal/eukaryal
           primase (AEP) superfamily. This group includes archaeal
           plasmids and bacteriophage AEPs. The ORF904 protein is a
           multifunctional protein having ATPase, primase and DNA
           polymerase activity, and may play a role in the
           replication of the archaeal plasmid. The pRN1 primpol
           domain exhibits DNA polymerase and primase activities; a
           cluster of active site residues (three acidic residues,
           and a histidine) is required for both these activities.
           For pRN1 primpol, the primase activity prefers dNTPs to
           rNTPs; incorporation of dNTPs requires rNTP as cofactor.
           The pRN1 primpol contains an unusual zinc-binding stem,
           which is not conserved in other members of this group..
          Length = 152

 Score = 58.9 bits (142), Expect = 5e-09
 Identities = 36/144 (25%), Positives = 51/144 (35%), Gaps = 11/144 (7%)

Query: 18  FKLIPLRLGDKRP-QRLGKWEEQLLSSEKIDKL----PACGFGFVCGVGEQPLYAFDIDS 72
           F +IPL  G KRP  +    +      E+I+      P    G   G     L   DID 
Sbjct: 1   FAVIPLDPGSKRPLIKGWPKDAATTDPEQIEAWWRDGPDANIGLRTGPSG--LVVIDIDV 58

Query: 73  KDEKTANTFK--DTFEILHGTPIVRIGQKPKILIPFRMNKEGIKKKKTTESTQGHLDILG 130
           K +  A      +  ++   T  VR G      + FR+  +G+  K         +DI G
Sbjct: 59  KHDGAAALAALAELGKLPPLTLTVRTG-SGGRHLYFRVP-DGVPVKSVKGKGGPGIDIRG 116

Query: 131 CGQYFVAYNIHPKTKKEYTWTTPP 154
            G Y VA          Y W +  
Sbjct: 117 GGGYVVAPPSVHPGGGYYVWKSTV 140


>gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
           VirB11, and related ATPases. The homohexamer, VirB11 is
           one of eleven Vir proteins, which are required for
           T-pilus biogenesis and virulence in the transfer of
           T-DNA from the Ti (tumor-inducing) plasmid of bacterial
           to plant cells. The pilus is a fibrous cell surface
           organelle, which mediates adhesion between bacteria
           during conjugative transfer or between bacteria and host
           eukaryotic cells during infection. VirB11- related
           ATPases include the archaeal flagella biosynthesis
           protein and the pilus assembly proteins CpaF/TadA and
           TrbB.  This alignment contains the C-terminal domain,
           which is the ATPase..
          Length = 186

 Score = 34.1 bits (78), Expect = 0.14
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 8/51 (15%)

Query: 471 DLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
           DL++    S     Y    V        +A++ I I G  GSGK+TL+N +
Sbjct: 3   DLIAQGTFSPLQAAYLWLAV--------EARKNILISGGTGSGKTTLLNAL 45


>gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system,
           ATPase component [Defense mechanisms].
          Length = 226

 Score = 33.6 bits (77), Expect = 0.24
 Identities = 12/19 (63%), Positives = 15/19 (78%)

Query: 503 FIHIRGVGGSGKSTLMNLI 521
           F+ I G  GSGKSTL+NL+
Sbjct: 33  FVAIVGPSGSGKSTLLNLL 51


>gnl|CDD|73014 cd03255, ABC_MJ0796_Lo1CDE_FtsE, This family is comprised of MJ0796
           ATP-binding cassette, macrolide-specific ABC-type efflux
           carrier (MacAB), and proteins involved in cell division
           (FtsE), and release of liporoteins from the cytoplasmic
           membrane (LolCDE).  They are clustered together
           phylogenetically.  MacAB is an exporter that confers
           resistance to macrolides, while the LolCDE system is not
           a transporter at all.  An FtsE null mutants showed
           filamentous growth and appeared viable on high salt
           medium only, indicating a role for FtsE in cell division
           and/or salt transport.  The LolCDE complex catalyses the
           release of lipoproteins from the cytoplasmic membrane
           prior to their targeting to the outer membrane..
          Length = 218

 Score = 33.2 bits (76), Expect = 0.28
 Identities = 11/19 (57%), Positives = 15/19 (78%)

Query: 503 FIHIRGVGGSGKSTLMNLI 521
           F+ I G  GSGKSTL+N++
Sbjct: 32  FVAIVGPSGSGKSTLLNIL 50


>gnl|CDD|30527 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
           recombination, and repair].
          Length = 935

 Score = 32.8 bits (75), Expect = 0.40
 Identities = 11/24 (45%), Positives = 13/24 (54%)

Query: 501 QRFIHIRGVGGSGKSTLMNLIKYA 524
             F  + GV GSGKSTL+N     
Sbjct: 627 GVFTCVTGVSGSGKSTLINDTLVP 650


>gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
           recombination, and repair].
          Length = 908

 Score = 31.9 bits (72), Expect = 0.65
 Identities = 44/282 (15%), Positives = 93/282 (32%), Gaps = 40/282 (14%)

Query: 506 IRGVGGSGKSTLMNLIKYA-FGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVII 564
           I G  G+GKS++++ I +A +G    + A + D +     ++         + G +  I 
Sbjct: 30  IVGPNGAGKSSILDAITFALYGKTPRLGAFSLDDLIRAGEKSASVE-LEFEVNGKKYRIE 88

Query: 565 SETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWW 624
            E       +   ++ +            G   ++        I     L     D   +
Sbjct: 89  REFRRGRGQSTGSLQIIEVD---------GERIADGKKDVNEKIEELLGL-----DKDTF 134

Query: 625 RRYIVIP---FDKPI----ANRDASFAQKLETKYTLEAKKWFLKGVKAYISKGLDV---- 673
            R + +P   FD  +      R     +    +   E     LK V       ++     
Sbjct: 135 TRSVYLPQGEFDAFLKSKPKERKEILDELFGLEK-YEKLSELLKEVIKEAKAKIEELEGQ 193

Query: 674 -----DIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESHSLAKSYSEYREQELNY 728
                +  E  L+A EEE +     +   ++     E L +E  +L +  +E  E++   
Sbjct: 194 LSELLEDIEDLLEALEEELKELKKLEEIQEE--QEEEELEQEIEALEERLAELEEEKERL 251

Query: 729 DRKRISTRTVTLNLKQKGF-----IGGIKREKIEKEWKSKRI 765
           +  +     +     +        +  ++R   E E K +R+
Sbjct: 252 EELKARLLEIESLELEALKIREEELRELERLLEELEEKIERL 293


>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
           nucleotide-binding domain (P-loop) near the N-terminus,
           participates in the maturation of the nickel center of
           carbon monoxide dehydrogenase (CODH). CODH from
           Rhodospirillum rubrum catalyzes the reversible oxidation
           of CO to CO2. CODH contains a nickel-iron-sulfur cluster
           (C-center) and an iron-sulfur cluster (B-center). CO
           oxidation occurs at the C-center. Three accessory
           proteins encoded by cooCTJ genes are involved in nickel
           incorporation into a nickel site. CooC functions as a
           nickel insertase that mobilizes nickel to apoCODH using
           energy released from ATP hydrolysis. CooC is a homodimer
           and has NTPase activities. Mutation at the P-loop
           abolishs its function..
          Length = 116

 Score = 31.3 bits (71), Expect = 1.1
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 504 IHIRGVGGSGKSTLMNLIKYAFGNQ----YVINAEASDIMQNRPPEAGKANPSLIRLM 557
           I I G GG GK+T+  L+      +      I+A+  D+    P         +  L+
Sbjct: 2   IAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPDDL----PERLSVEVGEIKLLL 55


>gnl|CDD|73030 cd03271, ABC_UvrA_II, The excision repair protein UvrA domain II;
           Nucleotide excision repair in eubacteria is a process
           that repairs DNA damage by the removal of a 12-13-mer
           oligonucleotide containing the lesion.  Recognition and
           cleavage of the damaged DNA is a multistep ATP-dependent
           reaction that requires the UvrA, UvrB, and UvrC
           proteins.  Both UvrA and UvrB are ATPases, with UvrA
           having two ATP binding sites, which have the
           characteristic signature of the family of ABC proteins
           and UvrB having one ATP binding site that is
           structurally related to that of helicases..
          Length = 261

 Score = 31.3 bits (71), Expect = 1.2
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 502 RFIHIRGVGGSGKSTLMNLIKYA 524
               + GV GSGKS+L+N   Y 
Sbjct: 22  VLTCVTGVSGSGKSSLINDTLYP 44


>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
           involved in the uptake of siderophores, heme, and
           vitamin B12, are widely conserved in bacteria and
           archaea.  Only very few species lack representatives of
           the siderophore family transporters.  The E. coli BtuCD
           protein is an ABC transporter mediating vitamin B12
           uptake.  The two ATP-binding cassettes (BtuD) are in
           close contact with each other, as are the two
           membrane-spanning subunits (BtuC); this arrangement is
           distinct from that observed for the E. coli lipid
           flippase MsbA.  The BtuC subunits provide 20
           transmembrane helices grouped around a translocation
           pathway that is closed to the cytoplasm by a gate
           region, whereas the dimer arrangement of the BtuD
           subunits resembles the ATP-bound form of the Rad50 DNA
           repair enzyme.  A prominent cytoplasmic loop of BtuC
           forms the contact region with the ATP-binding cassette
           and represent a conserved motif among the ABC
           transporters..
          Length = 180

 Score = 31.2 bits (71), Expect = 1.2
 Identities = 9/23 (39%), Positives = 14/23 (60%)

Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
           +A   + I G  G+GKSTL+  +
Sbjct: 23  EAGEIVGILGPNGAGKSTLLKTL 45


>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
           function prediction only].
          Length = 219

 Score = 30.7 bits (68), Expect = 1.7
 Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 1/52 (1%)

Query: 508 GVGGSGKSTLMN-LIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMG 558
           G GG GK+TL+N L+   F   Y       D  +   P        L    G
Sbjct: 12  GDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63


>gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
           [Coenzyme metabolism].
          Length = 231

 Score = 30.7 bits (69), Expect = 1.7
 Identities = 12/22 (54%), Positives = 15/22 (68%)

Query: 500 AQRFIHIRGVGGSGKSTLMNLI 521
           A   + I G  G+GKSTL+NLI
Sbjct: 24  AGEIVAILGPSGAGKSTLLNLI 45


>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
           thymidylate kinase, catalyzes the phosphorylation of
           thymidine monophosphate (TMP) to thymidine diphosphate
           (TDP) utilizing ATP as its preferred phophoryl donor.
           TMPK represents the rate-limiting step in either de novo
           or salvage biosynthesis of thymidine triphosphate
           (TTP)..
          Length = 200

 Score = 30.6 bits (69), Expect = 1.9
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 502 RFIHIRGVGGSGKSTLMNLIK 522
            FI   G+ G+GK+TL+ L+ 
Sbjct: 1   MFIVFEGIDGAGKTTLIELLA 21


>gnl|CDD|110446 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
           Helicase activity for this family has been demonstrated
           and NTPase activity. This helicase has multiple roles at
           different stages of viral RNA replication, as dissected
           by mutational analysis.
          Length = 226

 Score = 30.0 bits (68), Expect = 2.3
 Identities = 9/14 (64%), Positives = 10/14 (71%)

Query: 504 IHIRGVGGSGKSTL 517
           I + GV G GKSTL
Sbjct: 1   IVVHGVPGCGKSTL 14


>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
           cancer resistance protein) [Secondary metabolites
           biosynthesis, transport and catabolism].
          Length = 613

 Score = 30.3 bits (68), Expect = 2.3
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 21/57 (36%)

Query: 465 PSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
            ++  L  VSG  +  E++         A++G +            GSGK+TL+N +
Sbjct: 41  KTKTILKGVSGTAKPGELL---------AIMGPS------------GSGKTTLLNAL 76


>gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
           metabolism].
          Length = 208

 Score = 30.2 bits (68), Expect = 2.4
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 502 RFIHIRGVGGSGKSTLMNLIK 522
            FI I G+ G+GK+T   L+K
Sbjct: 4   MFIVIEGIDGAGKTTQAELLK 24


>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
           nucleotide-binding domain; ABC transporters are a large
           family of proteins involved in the transport of a wide
           variety of different compounds, like sugars, ions,
           peptides, and more complex organic molecules.  The
           nucleotide-binding domain shows the highest similarity
           between all members of the family.  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 157

 Score = 29.9 bits (67), Expect = 2.7
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
           KA   + + G  GSGKSTL+  I
Sbjct: 23  KAGEIVALVGPNGSGKSTLLRAI 45


>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
           an N-terminal double-glycine peptidase domain [Defense
           mechanisms].
          Length = 709

 Score = 29.8 bits (67), Expect = 3.1
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
                + I G  GSGKSTL+ L+
Sbjct: 497 PPGEKVAIVGRSGSGKSTLLKLL 519


>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance Protein)-like
           transporters are involved in drug, peptide, and lipid
           export.  They belong to the subfamily C of the
           ATP-binding cassette (ABC) superfamily of transport
           proteins.  The ABCC subfamily contains transporters with
           a diverse functional spectrum that includes ion
           transport, cell surface receptor, and toxin secretion
           activities.  The MRP-like family, simlar to all ABC
           proteins, have a common four-domain core structure
           constituted by two membrane-spanning domains, each
           composed of six transmembrane (TM) helices, and two
           nucleotide-binding domains (NBD).  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 171

 Score = 29.6 bits (67), Expect = 3.5
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
           K    + I G  GSGKSTL+ L+
Sbjct: 26  KPGEKVAIVGPSGSGKSTLLKLL 48


>gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment
           (EP) precursor transport, regulation of
           lipid-trafficking mechanisms, and pleiotropic drug
           resistance (DR).  DR is a well-described phenomenon
           occurring in fungi and shares several similarities with
           processes in bacteria and higher eukaryotes.  Compared
           to other members of the ABC transporter subfamilies, the
           ABCG transporter family is composed of proteins that
           have an ATP-binding cassette domain at the N-terminus
           and a TM (transmembrane) domain at the C-terminus..
          Length = 194

 Score = 29.4 bits (66), Expect = 3.6
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 502 RFIHIRGVGGSGKSTLMNLI 521
               I G  G+GKSTL+N +
Sbjct: 36  ELTAIMGPSGAGKSTLLNAL 55


>gnl|CDD|31313 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
           system, ATPase component [Inorganic ion transport and
           metabolism].
          Length = 248

 Score = 29.4 bits (66), Expect = 3.7
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 503 FIHIRGVGGSGKSTLMNLI 521
           F+ I G  G GKSTL+ LI
Sbjct: 31  FVAILGPSGCGKSTLLRLI 49


>gnl|CDD|34593 COG4988, CydD, ABC-type transport system involved in cytochrome bd
           biosynthesis, ATPase and permease components [Energy
           production and conversion / Posttranslational
           modification, protein turnover, chaperones].
          Length = 559

 Score = 29.4 bits (66), Expect = 3.8
 Identities = 11/23 (47%), Positives = 16/23 (69%)

Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
           KA +   + G  G+GKSTL+NL+
Sbjct: 345 KAGQLTALVGASGAGKSTLLNLL 367


>gnl|CDD|30197 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
           involved in the metabolism of nicotinamide adenine
           dinucleotide (NAD+). This enzyme catalyzes the
           phosphorylation of nicotinamide riboside (NR) to form
           nicotinamide mononucleotide (NMN). It defines the NR
           salvage pathway of NAD+ biosynthesis in addition to the
           pathways through nicotinic acid mononucleotide (NaMN).
           This enzyme can also phosphorylate the anticancer drug
           tiazofurin, which is an analog of nicotinamide
           riboside..
          Length = 187

 Score = 29.5 bits (66), Expect = 4.2
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 504 IHIRGVGGSGKSTLMNLIKYAFGNQYVIN 532
           + I GV  SGK+TL  L++    N  VI+
Sbjct: 2   VGISGVTNSGKTTLAKLLQRILPNCCVIH 30


>gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_transporters, NrtD and SsuB are the
           ATP-binding subunits of the bacterial ABC-type nitrate
           and sulfonate transport systems, respectively.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides, and more complex organic
           molecules.  The nucleotide binding domain shows the
           highest similarity between all members of the family.
           ABC transporters are a subset of nucleotide hydrolases
           that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to, the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 220

 Score = 29.3 bits (66), Expect = 4.2
 Identities = 9/19 (47%), Positives = 13/19 (68%)

Query: 503 FIHIRGVGGSGKSTLMNLI 521
           F+ + G  G GKSTL+ +I
Sbjct: 32  FVALVGPSGCGKSTLLRII 50


>gnl|CDD|72986 cd03227, ABC_Class2, ABC-type Class 2 contains systems involved in
           cellular processes other than transport.  These families
           are characterised by the fact that the ABC subunit is
           made up of duplicated, fused ABC modules (ABC2).  No
           known transmembrane proteins or domains are associated
           with these proteins..
          Length = 162

 Score = 29.2 bits (65), Expect = 4.3
 Identities = 11/31 (35%), Positives = 14/31 (45%)

Query: 500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV 530
                 I G  GSGKST+++ I  A G    
Sbjct: 20  EGSLTIITGPNGSGKSTILDAIGLALGGAQS 50


>gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
           expression and maturation of urease and hydrogenase
           [Posttranslational modification, protein turnover,
           chaperones / Transcription].
          Length = 202

 Score = 29.0 bits (65), Expect = 5.0
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 9/87 (10%)

Query: 498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLM 557
           N+    I + G  GSGK+ L+     A  ++Y I     DI      +       L +L 
Sbjct: 10  NRPMLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGDIYTKEDADR------LRKLP 63

Query: 558 GSRIVII---SETNENDEINAAKIKQM 581
           G  I+ +      + +  +N   I+++
Sbjct: 64  GEPIIGVETGKGCHLDASMNLEAIEEL 90


>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
           transporters homologous to the Drosophila white gene,
           which acts as a dimeric importer for eye pigment
           precursors.  The eye pigmentation of Drosophila is
           developed from the synthesis and deposition in the cells
           of red pigments, which are synthesized from guanine, and
           brown pigments, which are synthesized from tryptophan.
           The pigment precursors are encoded by the white, brown,
           and scarlet genes, respectively.  Evidence from genetic
           and biochemical studies suggest that the White and Brown
           proteins function as heterodimers to import guanine,
           while the White and Scarlet proteins function to import
           tryptophan.  However, a recent study also suggests that
           White may be involved in the transport of a metabolite,
           such as 3-hydroxykynurenine, across intracellular
           membranes.  Mammalian ABC transporters belonging to the
           White subfamily (ABCG1, ABCG5, and ABCG8) have been
           shown to be involved in the regulation of
           lipid-trafficking mechanisms in macrophages,
           hepatocytes, and intestinal mucosa cells.  ABCG1 (ABC8),
           the human homolog of the Drosophila white gene is
           induced in monocyte-derived macrophages during
           cholesterol influx mediated by acetylated low-density
           lipoprotein.  It is possible that human ABCG1 forms
           heterodimers with several heterologous partners..
          Length = 226

 Score = 29.0 bits (65), Expect = 5.2
 Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 27/74 (36%)

Query: 473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI------KYAFG 526
           VS + ES +VM         A+LG +            GSGK+TL++ I           
Sbjct: 26  VSLHVESGQVM---------AILGSS------------GSGKTTLLDAISGRVEGGGTTS 64

Query: 527 NQYVINAEASDIMQ 540
            Q + N +     Q
Sbjct: 65  GQILFNGQPRKPDQ 78


>gnl|CDD|73034 cd03275, ABC_SMC1_euk, Eukaryotic SMC1 proteins; SMC proteins are
           large (approximately 110 to 170 kDa), and each is
           arranged into five recognizable domains.  Amino-acid
           sequence homology of SMC proteins between species is
           largely confined to the amino- and carboxy-terminal
           globular domains. The amino-terminal domain contains a
           'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
           single-letter amino-acid code), which by mutational
           studies has been shown to be essential in several
           proteins.  The carboxy-terminal domain contains a
           sequence (the DA-box) that resembles a 'Walker B' motif,
           and a motif with homology to the signature sequence of
           the ATP-binding cassette (ABC) family of ATPases.  The
           sequence homology within the carboxy-terminal domain is
           relatively high within the SMC1-SMC4 group, whereas SMC5
           and SMC6 show some divergence in both of these
           sequences.  In eukaryotic cells, the proteins are found
           as heterodimers of SMC1 paired with SMC3, SMC2 with
           SMC4, and SMC5 with SMC6 (formerly known as Rad18)..
          Length = 247

 Score = 29.0 bits (65), Expect = 5.4
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 502 RFIHIRGVGGSGKSTLMNLIKYAFG 526
           RF  I G  GSGKS LM+ I +  G
Sbjct: 23  RFTCIIGPNGSGKSNLMDAISFVLG 47


>gnl|CDD|33194 COG3387, SGA1, Glucoamylase and related glycosyl hydrolases
           [Carbohydrate transport and metabolism].
          Length = 612

 Score = 28.8 bits (64), Expect = 5.4
 Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 14/82 (17%)

Query: 320 KKGHFLYTADTK----------AWYKKDKNNVYIWSLTLDKITASIMNFLVSMKEDVFDL 369
           + GHF YT  T           A    DK +   W  T D++  +++    +     F  
Sbjct: 411 RGGHFTYTKATVYAGLDAAADLAEEFGDKGSAEHWRKTADELKEAVLRRGYAEDGGYFVR 470

Query: 370 SEEPEDNNKNSKS----PRFWF 387
           S   + ++    S      F F
Sbjct: 471 SLGRKPDDTVDASLLGLVLFGF 492


>gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
           division and chromosome partitioning].
          Length = 223

 Score = 29.0 bits (65), Expect = 5.5
 Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 10/42 (23%)

Query: 490 VGMALLGGNKAQR----------FIHIRGVGGSGKSTLMNLI 521
           V  A  GG +A R          F+ + G  G+GKSTL+ LI
Sbjct: 7   VSKAYPGGREALRDVSFHIPKGEFVFLTGPSGAGKSTLLKLI 48


>gnl|CDD|30586 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
          Length = 201

 Score = 28.7 bits (64), Expect = 6.2
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVI 563
           I + G  GSGKST+  ++        VI+  A D+ +      G+A   +    G  I  
Sbjct: 5   IGLTGGIGSGKSTVAKILAE--LGFPVID--ADDVAREVVEPGGEALQEIAERFGLEI-- 58

Query: 564 ISETNENDEINAAKIKQMTGGD 585
               +E+  ++  K+++    D
Sbjct: 59  ---LDEDGGLDRRKLREKVFND 77


>gnl|CDD|73013 cd03254, ABCC_Glucan_exporter_like, Glucan exporter ATP-binding
           protein.  In A. tumefaciens cyclic beta-1, 2-glucan must
           be transported into the periplasmic space to exert its
           action as a virluence factor.  This subfamily belongs to
           the MRP-like family and is involved in drug, peptide,
           and lipid export.  The MRP-like family, similar to all
           ABC proteins, have a common four-domain core structure
           constituted by two membrane-spanning domains each
           composed of six transmembrane (TM) helices and two
           nucleotide-binding domains (NBD).  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 229

 Score = 28.6 bits (64), Expect = 6.6
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
           K    + I G  G+GK+TL+NL+
Sbjct: 27  KPGETVAIVGPTGAGKTTLINLL 49


>gnl|CDD|34687 COG5083, SMP2, Uncharacterized protein involved in plasmid
           maintenance [General function prediction only].
          Length = 580

 Score = 28.5 bits (63), Expect = 6.7
 Identities = 41/207 (19%), Positives = 63/207 (30%), Gaps = 34/207 (16%)

Query: 255 KQGSTYDEENFNYKWDTFDFEEIGDTAKKRS--TFTSLFYHHG------------KLIPK 300
             GS   + NF+         +IG     R+  T  +    +G             L  K
Sbjct: 125 GSGSDLSKLNFDIVLKEPKNLDIGFRKYSRNKRTENTGKRMYGQSSRQRGHKDSYHLFEK 184

Query: 301 GLLASRFSDAYNKA---MFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMN 357
             +  +F    NK    M  I+K           + YK   N +   S+  D+ T+    
Sbjct: 185 RFV--KFGSLLNKTLHFMSLIFKTKTNGDLLTDISLYKPGGNKILDLSVN-DRDTSKDEF 241

Query: 358 FLVSMKEDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQNVEENSKAKSTAQSLEAGSIFS- 416
           F     E       +PED   NS   R      +   N  +    K+  QS+    ++S 
Sbjct: 242 FDFKDIE-----FVKPEDTEFNSWINREHVTKLHPHHNGSDEVYGKNPPQSISGDFLYSD 296

Query: 417 --------ITSDLLDSSSRFLGEQDGI 435
                     S L  S S      + I
Sbjct: 297 VRVSLANDEVSILEYSHSSSEPSWNKI 323


>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components
           [Carbohydrate transport and metabolism].
          Length = 338

 Score = 28.7 bits (64), Expect = 7.1
 Identities = 9/19 (47%), Positives = 13/19 (68%)

Query: 503 FIHIRGVGGSGKSTLMNLI 521
           F+ + G  G GKSTL+ +I
Sbjct: 31  FVVLLGPSGCGKSTLLRMI 49


>gnl|CDD|31316 COG1119, ModF, ABC-type molybdenum transport system, ATPase
           component/photorepair protein PhrA [Inorganic ion
           transport and metabolism].
          Length = 257

 Score = 28.7 bits (64), Expect = 7.4
 Identities = 8/17 (47%), Positives = 13/17 (76%)

Query: 505 HIRGVGGSGKSTLMNLI 521
            I G  G+GK+TL++L+
Sbjct: 61  AIVGPNGAGKTTLLSLL 77


>gnl|CDD|111487 pfam02594, DUF167, Uncharacterized ACR, YggU family COG1872. 
          Length = 78

 Score = 28.3 bits (64), Expect = 7.4
 Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 7/30 (23%)

Query: 543 PPEAGKANPSLIRLMG-------SRIVIIS 565
           PP  GKAN  LI+ +        S + I+S
Sbjct: 36  PPVDGKANAELIKFLAKTLGVPKSDVEIVS 65


>gnl|CDD|35241 KOG0018, KOG0018, KOG0018, Structural maintenance of chromosome
           protein 1 (sister chromatid cohesion complex Cohesin,
           subunit SMC1) [Cell cycle control, cell division,
           chromosome partitioning].
          Length = 1141

 Score = 28.3 bits (63), Expect = 8.2
 Identities = 13/26 (50%), Positives = 15/26 (57%)

Query: 501 QRFIHIRGVGGSGKSTLMNLIKYAFG 526
            RF  I G  GSGKS LM+ I +  G
Sbjct: 25  DRFTAIIGPNGSGKSNLMDAISFVLG 50


>gnl|CDD|33900 COG4148, ModC, ABC-type molybdate transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 352

 Score = 28.3 bits (63), Expect = 8.4
 Identities = 9/22 (40%), Positives = 15/22 (68%)

Query: 500 AQRFIHIRGVGGSGKSTLMNLI 521
           A+    + G  GSGK++L+N+I
Sbjct: 23  ARGITALFGPSGSGKTSLINMI 44


>gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component
           [Carbohydrate transport and metabolism].
          Length = 500

 Score = 28.2 bits (63), Expect = 8.4
 Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 12/30 (40%)

Query: 492 MALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
            ALLG N            G+GKSTLM ++
Sbjct: 37  HALLGEN------------GAGKSTLMKIL 54


>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
           a cobalt transport family found in bacteria, archaea,
           and eukaryota.  The transition metal cobalt is an
           essential component of many enzymes and must be
           transported into cells in appropriate amounts when
           needed.  This ABC transport system of the CbiMNQO family
           is involved in cobalt transport in association with the
           cobalamin (vitamin B12) biosynthetic pathways.  Most of
           cobalt (Cbi) transport systems possess a separate CbiN
           component, the cobalt-binding periplasmic protein, and
           they are encoded by the conserved gene cluster cbiMNQO. 
           Both the CbiM and CbiQ proteins are integral cytoplasmic
           membrane proteins, and the CbiO protein has the linker
           peptide and the Walker A and B motifs commonly found in
           the ATPase components of the ABC-type transport
           systems..
          Length = 211

 Score = 28.2 bits (63), Expect = 9.1
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 503 FIHIRGVGGSGKSTLMNLI 521
           F+ I G  GSGKSTL+ L+
Sbjct: 29  FVLIVGPNGSGKSTLLRLL 47


>gnl|CDD|147768 pfam05794, Tcp11, T-complex protein 11.  This family consists of
           several eukaryotic T-complex protein 11 (Tcp11) related
           sequences. Tcp11 is only expressed in fertile adult
           mammalian testes and is thought to be important in sperm
           function and fertility. The family also contains the
           yeast Sok1 protein which is known to suppress cyclic
           AMP-dependent protein kinase mutants.
          Length = 423

 Score = 28.0 bits (63), Expect = 9.2
 Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 3/35 (8%)

Query: 163 PLLSEEDVEYLFKFFQEITVPLVKDKKSIIPSKTW 197
           PLL E  VEY  K FQE+   L +   S+  +K W
Sbjct: 160 PLLIENSVEYERKKFQEL---LEEAPNSLPLTKKW 191


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.316    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0745    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 9,783,549
Number of extensions: 528045
Number of successful extensions: 1495
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1490
Number of HSP's successfully gapped: 62
Length of query: 789
Length of database: 6,263,737
Length adjustment: 102
Effective length of query: 687
Effective length of database: 4,059,619
Effective search space: 2788958253
Effective search space used: 2788958253
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.2 bits)