RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780766|ref|YP_003065179.1| recombination protein F
[Candidatus Liberibacter asiaticus str. psy62]
         (375 letters)



>gnl|CDD|31388 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
           [DNA replication, recombination, and repair].
          Length = 363

 Score =  288 bits (739), Expect = 2e-78
 Identities = 122/366 (33%), Positives = 189/366 (51%), Gaps = 9/366 (2%)

Query: 5   IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADV 64
           + +  L +  FRNYA L L       + VG+NG GKTN+LEAI  L+ GR  R +   ++
Sbjct: 1   MYLLSLLLRNFRNYAELDLDLSPGVNVLVGENGQGKTNLLEAIYLLALGRSHRTSRDKEL 60

Query: 65  TRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISW 124
            R G+       ARV+       + +++  +  R VR   IN    R + EL  HL +  
Sbjct: 61  IRTGADEAEI-SARVQRKGREGTLGLQISKKGRRRVR---INGTKARKLAELAGHLNVVL 116

Query: 125 LVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCS 184
             P    +  G   +RRRFLD ++F I+P +   + ++E+L++ RN LL +   D +W  
Sbjct: 117 FTPEDLGLVKGSPSDRRRFLDWLLFQIEPVYLEALSNYEKLLKQRNALLKQLQGDYAWLD 176

Query: 185 SIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCALK 244
             + Q+AELG +I  AR E +NAL+ L  +  Q   F     SL+ F  G  D +   ++
Sbjct: 177 VWDQQLAELGAEIAAARAEYLNALAPLAEKIHQL--FLPELESLSIFYRGSVDVTAWEIE 234

Query: 245 EEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHA 304
           E+Y + L   R+ D     TL+GPHR DL+     K       S G+QK + + + LA  
Sbjct: 235 EDYLEALAKRRERDLARGYTLVGPHRDDLLFRLNGKPA-ADFASQGQQKTLALALRLAEI 293

Query: 305 RLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDS-LNETAK 363
            L+   TG  PILLLD++++ LD+ +R AL     ++G Q+F+T TD    D  L+E A+
Sbjct: 294 ELLREETGEYPILLLDDVASELDDGRRAALLDT-IELGVQVFVTTTDLEDIDDNLDENAQ 352

Query: 364 FMRISN 369
              + +
Sbjct: 353 MFHVED 358


>gnl|CDD|73001 cd03242, ABC_RecF, RecF is a recombinational DNA repair ATPase that
           maintains replication in the presence of DNA damage.
           When replication is prematurely disrupted by DNA damage,
           several recF pathway gene products play critical roles
           processing the arrested replication fork, allowing it to
           resume and complete its task.  This CD represents the
           nucleotide binding domain of RecF.  RecF  belongs to a
           large superfamily of ABC transporters involved in the
           transport of a wide variety of different compounds
           including 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 with 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 = 270

 Score =  147 bits (372), Expect = 6e-36
 Identities = 53/167 (31%), Positives = 89/167 (53%), Gaps = 4/167 (2%)

Query: 7   IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR 66
           +K L +  FRNYA L L F+   T+ VG+N  GKTN+LEAIS L+ G+  R +   ++ R
Sbjct: 1   LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIR 60

Query: 67  IGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLV 126
            G+     + A +E   G   + + + +   R  R   +N + +R + +L   L   W  
Sbjct: 61  WGAEEAKIS-AVLERQGGELALELTIRSGGGRKAR---LNGIKVRRLSDLLGVLNAVWFA 116

Query: 127 PSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLL 173
           P    +  G   +RRRFLDR++  ++P +   + ++++ +R RN LL
Sbjct: 117 PEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRNALL 163



 Score = 97.6 bits (243), Expect = 5e-21
 Identities = 44/135 (32%), Positives = 67/135 (49%), Gaps = 3/135 (2%)

Query: 236 FDQSFCALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVV 295
            D+    L+  YA  L + +K        L GPHR DL+    DK      GS G+Q+ +
Sbjct: 134 LDRLLGQLEPAYAHVLSEYQKALRQRNALLKGPHRDDLLFFLNDKPAA-DFGSQGQQRTL 192

Query: 296 LVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355
            + + LA  +LI   +G  P+LLLD++ A LD  ++ AL   +     Q F+T TD + F
Sbjct: 193 ALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAIEGRV-QTFVTTTDLADF 251

Query: 356 DSL-NETAKFMRISN 369
           D+L    A+  R+  
Sbjct: 252 DALWLRRAQIFRVDA 266


>gnl|CDD|145545 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain.  This domain
          is found at the N terminus of SMC proteins. The SMC
          (structural maintenance of chromosomes) superfamily
          proteins have ATP-binding domains at the N- and
          C-termini, and two extended coiled-coil domains
          separated by a hinge in the middle. The eukaryotic SMC
          proteins form two kind of heterodimers: the SMC1/SMC3
          and the SMC2/SMC4 types. These heterodimers constitute
          an essential part of higher order complexes, which are
          involved in chromatin and DNA dynamics. This family
          also includes the RecF and RecN proteins that are
          involved in DNA metabolism and recombination.
          Length = 1162

 Score = 48.4 bits (115), Expect = 3e-06
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 6  KIKFLNISEFRNYA-SLRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASY 61
           +K + I  F++YA ++ L F    T  VG NG GK+NIL+AI F       +  R    
Sbjct: 1  YLKRIEIEGFKSYAKTVILPFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKSLRSERL 60

Query: 62 ADVTRIGSPSFFSTFARVE 80
          +D+        F   A V 
Sbjct: 61 SDLIHYSKSGAFVNSAEVT 79


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

 Score = 41.6 bits (97), Expect = 4e-04
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 6  KIKFLNISEFRNYA--SLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPG--RGFRRASY 61
          KI  L +  FR++    +  +FD+   + VG NG GK++IL+AI+F   G        S 
Sbjct: 2  KILRLRLKNFRSFKDIDIEKLFDSGIFLIVGPNGAGKSSILDAITFALYGKTPRLGAFSL 61

Query: 62 ADVTRIGS 69
           D+ R G 
Sbjct: 62 DDLIRAGE 69



 Score = 35.0 bits (80), Expect = 0.032
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 272 DLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKR 331
            ++V    +   I   S GE+ +  + + LA + L+        +L LDE    LDE++ 
Sbjct: 801 VVVVYDGGEVRPIKTLSGGERFLASLALRLALSDLLQGRAR-LELLFLDEPFGTLDEERL 859

Query: 332 NALFRIVTDIGSQIFMTG 349
             L  I+ ++ S      
Sbjct: 860 EKLAEILEELLSDGRQII 877


>gnl|CDD|31303 COG1106, COG1106, Predicted ATPases [General function prediction
          only].
          Length = 371

 Score = 41.2 bits (96), Expect = 5e-04
 Identities = 18/45 (40%), Positives = 25/45 (55%)

Query: 7  IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLS 51
          IK   I  F+++  L L    +  I  G NG GK+N+LEA+ FL 
Sbjct: 2  IKSFKIKNFKSFRELELEDFGKINIIYGANGAGKSNLLEALYFLK 46


>gnl|CDD|73037 cd03278, ABC_SMC_barmotin, Barmotin is a tight
          junction-associated protein expressed in rat epithelial
          cells which is thought to have an important regulatory
          role in tight junction barrier function.  Barmotin
          belongs to the SMC protein family.  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 = 197

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 7  IKFLNISEFRNYAS-LRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASYA 62
          +K L +  F+++A    + F    T  VG NG GK+NI++AI +       +  R    +
Sbjct: 1  LKKLELKGFKSFADKTTIPFPPGLTAIVGPNGSGKSNIIDAIRWVLGEQSAKSLRGEKMS 60

Query: 63 DVTRIGS 69
          DV   GS
Sbjct: 61 DVIFAGS 67


>gnl|CDD|31389 COG1196, Smc, Chromosome segregation ATPases [Cell division and
          chromosome partitioning].
          Length = 1163

 Score = 38.1 bits (88), Expect = 0.004
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 5  IKIKFLNISEFRNYAS-LRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRAS 60
          + +K + +  F+++A    + F    T  VG NG GK+NI++AI F       +  R + 
Sbjct: 1  MYLKRIELKGFKSFADPTEINFSPGFTAIVGPNGSGKSNIVDAIRFVLGEQSAKNLRASK 60

Query: 61 YADVTRIGS 69
           +D+   GS
Sbjct: 61 MSDLIFAGS 69


>gnl|CDD|72999 cd03240, ABC_Rad50, The catalytic domains of Rad50 are similar to
          the ATP-binding cassette of ABC transporters, but are
          not associated with membrane-spanning domains.  The
          conserved ATP-binding motifs common to Rad50 and the
          ABC transporter family include the Walker A and Walker
          B motifs, the Q loop, a histidine residue in the switch
          region, a D-loop, and a conserved LSGG sequence.  This
          conserved sequence, LSGG, is the most specific and
          characteristic motif of this family and is thus known
          as the ABC signature sequence..
          Length = 204

 Score = 37.9 bits (88), Expect = 0.005
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 7  IKFLNISEFRNYAS-LRLVFDAQHTIFVGDNGVGKTNILEAISF----LSPGRGFRRASY 61
          I  L+I   R++     + F +  T+ VG NG GKT I+EA+ +      P      A  
Sbjct: 1  IDKLSIRNIRSFHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYALTGELPPNSKGGAHD 60

Query: 62 ADVTRIGS 69
            + R G 
Sbjct: 61 PKLIREGE 68



 Score = 31.7 bits (72), Expect = 0.31
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 4/58 (6%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKR-NALFRIVTDIGSQ 344
           S GE+ +  + I LA A           IL LDE + +LDE+    +L  I+ +  SQ
Sbjct: 117 SGGEKVLASLIIRLALAETFG---SNCGILALDEPTTNLDEENIEESLAEIIEERKSQ 171


>gnl|CDD|73031 cd03272, ABC_SMC3_euk, Eukaryotic SMC3 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 = 243

 Score = 36.7 bits (85), Expect = 0.010
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 7  IKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50
          IK + I  F++Y    ++  F  +H + VG NG GK+N   AI F+
Sbjct: 1  IKQVIIQGFKSYKDQTVIEPFSPKHNVVVGRNGSGKSNFFAAIRFV 46



 Score = 27.9 bits (62), Expect = 5.2
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 279 DKAITIAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           D+   +   S G++ +V + +  A  +        AP  L DEI A LD   R A+  ++
Sbjct: 151 DEQQEMQQLSGGQKSLVALALIFAIQKCDP-----APFYLFDEIDAALDAQYRTAVANMI 205

Query: 339 TDIGSQI-FMTGT 350
            ++     F+T T
Sbjct: 206 KELSDGAQFITTT 218


>gnl|CDD|33393 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
          family [DNA replication, recombination, and repair].
          Length = 581

 Score = 36.1 bits (83), Expect = 0.015
 Identities = 13/46 (28%), Positives = 26/46 (56%)

Query: 5  IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFL 50
          + ++ + I  FR    L L F+    + +G+N  GK+++L+A+  L
Sbjct: 1  MHLERVKIKNFRGINRLSLEFEEGLNVLIGENNSGKSSLLDALRLL 46


>gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome
          protein 2 (chromosome condensation complex Condensin,
          subunit E) [Chromatin structure and dynamics, Cell
          cycle control, cell division, chromosome partitioning].
          Length = 1174

 Score = 36.1 bits (83), Expect = 0.016
 Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%)

Query: 5  IKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50
          + IK + +  F++YA+  ++  FD Q     G NG GK+NIL++I F+
Sbjct: 1  MHIKEIILDGFKSYATRTVISGFDPQFNAITGLNGSGKSNILDSICFV 48


>gnl|CDD|33697 COG3910, COG3910, Predicted ATPase [General function prediction
          only].
          Length = 233

 Score = 36.0 bits (83), Expect = 0.017
 Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 11 NISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS 48
          ++  FR +   RL F A  T   G+NG GK+ +LEAI+
Sbjct: 22 SLPAFR-HLEERLEFRAPITFITGENGSGKSTLLEAIA 58


>gnl|CDD|73032 cd03273, ABC_SMC2_euk, Eukaryotic SMC2 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 = 251

 Score = 36.0 bits (83), Expect = 0.018
 Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%)

Query: 5  IKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50
          + IK + +  F++YA+  ++  FD Q     G NG GK+NIL+AI F+
Sbjct: 1  MHIKEIILDGFKSYATRTVISGFDPQFNAITGLNGSGKSNILDAICFV 48


>gnl|CDD|72998 cd03239, ABC_SMC_head, The structural maintenance of chromosomes
          (SMC) proteins are essential for successful chromosome
          transmission during replication and segregation of the
          genome in all organisms.  SMCs are generally present as
          single proteins in bacteria, and as at least six
          distinct proteins in eukaryotes.  The proteins range in
          size from approximately 110 to 170 kDa, and each has
          five distinct domains: amino- and carboxy-terminal
          globular domains, which contain sequences
          characteristic of ATPases, two coiled-coil regions
          separating the terminal domains , and a central
          flexible hinge.  SMC proteins function together with
          other proteins in a range of chromosomal transactions,
          including chromosome condensation, sister-chromatid
          cohesion, recombination, DNA repair, and epigenetic
          silencing of gene expression..
          Length = 178

 Score = 35.2 bits (81), Expect = 0.026
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 7  IKFLNISEFRNYASLRLV-FDAQHTIFVGDNGVGKTNILEAISFLSPGR 54
          IK + +  F++Y    +V         VG NG GK+NI++AI F+  G+
Sbjct: 1  IKQITLKNFKSYRDETVVGGSNSFNAIVGPNGSGKSNIVDAICFVLGGK 49


>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 = 35.3 bits (81), Expect = 0.027
 Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 3/46 (6%)

Query: 6  KIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISF 49
          ++  L I  F++Y   +++  FD + T  +G NG GK+N+++AISF
Sbjct: 3  RLLTLEIENFKSYKGHQVIGPFD-RFTAIIGPNGSGKSNLMDAISF 47


>gnl|CDD|33731 COG3950, COG3950, Predicted ATP-binding protein involved in
          virulence [General function prediction only].
          Length = 440

 Score = 35.0 bits (80), Expect = 0.035
 Identities = 16/45 (35%), Positives = 29/45 (64%), Gaps = 1/45 (2%)

Query: 5  IKIKFLNISEFRNYASLRLVFDAQH-TIFVGDNGVGKTNILEAIS 48
          ++++ ++++ FR + +L + F     TI VG NG GKT +L+AI 
Sbjct: 1  MRLRKISLNNFRCFLNLDITFGESETTIIVGPNGSGKTTVLDAIR 45


>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 = 34.9 bits (80), Expect = 0.038
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 14/102 (13%)

Query: 25  FDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR---IGSPSFFSTFARVE- 80
            +   TI  G NG GK+ IL+AI     G        + V     + + S    F R++ 
Sbjct: 19  GEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAELIFTRLQL 78

Query: 81  --GMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHL 120
             G + L+ +++ L            +    + ++DE+++ L
Sbjct: 79  SGGEKELSALALILALAS--------LKPRPLYILDEIDRGL 112



 Score = 29.5 bits (66), Expect = 1.5
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 5/51 (9%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           S GE+++  + + LA A     +    P+ +LDEI   LD     AL   +
Sbjct: 79  SGGEKELSALALILALA-----SLKPRPLYILDEIDRGLDPRDGQALAEAI 124


>gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome
           protein 4 (chromosome condensation complex Condensin,
           subunit C) [Chromatin structure and dynamics, Cell cycle
           control, cell division, chromosome partitioning].
          Length = 1293

 Score = 34.9 bits (80), Expect = 0.041
 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 2   TNRIKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57
             R+ I  + +  F++YA  +++  F    T  VG NG GK+N+++++ F+    GFR
Sbjct: 81  GPRLMITEIVVENFKSYAGKQILGPFHKSFTAIVGPNGSGKSNVIDSMLFVF---GFR 135


>gnl|CDD|36182 KOG0964, KOG0964, KOG0964, Structural maintenance of chromosome
          protein 3 (sister chromatid cohesion complex Cohesin,
          subunit SMC3) [Cell cycle control, cell division,
          chromosome partitioning].
          Length = 1200

 Score = 34.6 bits (79), Expect = 0.050
 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 5  IKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50
          + IK + I  FR+Y    +V  F   H + VG NG GK+N   AI F+
Sbjct: 1  MYIKQVIIKGFRSYRDETVVDPFSPHHNVIVGRNGSGKSNFFHAIRFV 48


>gnl|CDD|30843 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
          recombination, and repair].
          Length = 557

 Score = 34.4 bits (79), Expect = 0.055
 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 5/55 (9%)

Query: 1  MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRG 55
          M   + IK   I E      L L F+   T+  G+ G GK+ I++A+  L  GR 
Sbjct: 1  MLLELSIKNFAIIE-----ELELEFEKGLTVLTGETGAGKSIIIDALGLLLGGRA 50


>gnl|CDD|73000 cd03241, ABC_RecN, RecN ATPase involved in DNA repair; 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 including 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 = 276

 Score = 34.0 bits (78), Expect = 0.067
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 10 LNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIG 68
          L+I  F     L L F+   T+  G+ G GK+ +L+A+S L  GR     + AD+ R G
Sbjct: 4  LSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGR-----ASADLIRSG 57


>gnl|CDD|73051 cd03292, ABC_FtsE_transporter, FtsE is a hydrophilic
           nucleotide-binding protein that binds FtsX to form a
           heterodimeric ATP-binding cassette (ABC)-type
           transporter that associates with the bacterial inner
           membrane.  The FtsE/X transporter is thought to be
           involved in cell division and is important for assembly
           or stability of the septal ring..
          Length = 214

 Score = 33.7 bits (77), Expect = 0.077
 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 13/87 (14%)

Query: 275 VDYCDKAITIAHG-STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNA 333
           V    K   +    S GEQ+ V +      AR I N+     IL+ DE + +LD D    
Sbjct: 124 VGLSHKHRALPAELSGGEQQRVAI------ARAIVNS---PTILIADEPTGNLDPDTTWE 174

Query: 334 LFRIVTDI---GSQIFMTGTDKSVFDS 357
           +  ++  I   G+ + +    K + D+
Sbjct: 175 IMNLLKKINKAGTTVVVATHAKELVDT 201


>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 = 33.2 bits (76), Expect = 0.10
 Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 7  IKFLNISEFRNYASLRLV-FDAQHTIFVGDNGVGKTNILEAISF 49
          +K L +  F++Y    ++    + T  +G NG GK+N+++AISF
Sbjct: 1  LKRLELENFKSYKGRHVIGPFDRFTCIIGPNGSGKSNLMDAISF 44


>gnl|CDD|34256 COG4637, COG4637, Predicted ATPase [General function prediction
          only].
          Length = 373

 Score = 32.6 bits (74), Expect = 0.20
 Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 6  KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFL 50
           +  + +  +R++ SL L    +  + +G NG GK+N  +A+  L
Sbjct: 2  MLVSIKVKNYRSFRSLDLEI-RRVNVIIGANGAGKSNFYDALRLL 45


>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 = 32.2 bits (73), Expect = 0.23
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 12/64 (18%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI---GSQ 344
           S G+++ V +   L              +LLLDE ++ LD   R  L  ++ ++   G  
Sbjct: 82  SGGQRQRVALARALLLN---------PDLLLLDEPTSGLDPASRERLLELLRELAEEGRT 132

Query: 345 IFMT 348
           + + 
Sbjct: 133 VIIV 136



 Score = 30.3 bits (68), Expect = 0.87
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 24 VFDAQHTIFVGDNGVGKTNILEAISFL-SPGRGFRRASYADVTRIGSPSFFSTFARVEGM 82
          +   +    VG NG GK+ +L AI+ L  P  G       D+ ++           V  +
Sbjct: 22 LKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQL 81

Query: 83 EG 84
           G
Sbjct: 82 SG 83


>gnl|CDD|73033 cd03274, ABC_SMC4_euk, Eukaryotic SMC4 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 = 212

 Score = 31.7 bits (72), Expect = 0.33
 Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 5/53 (9%)

Query: 7  IKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57
          I  L +  F++YA  +++  F    +  VG NG GK+N+++++ F+    GFR
Sbjct: 3  ITKLVLENFKSYAGEQVIGPFHKSFSAIVGPNGSGKSNVIDSMLFVF---GFR 52


>gnl|CDD|33894 COG4138, BtuD, ABC-type cobalamin transport system, ATPase
           component [Coenzyme metabolism].
          Length = 248

 Score = 31.5 bits (71), Expect = 0.43
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 283 TIAHGSTGE-QKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341
           +    S GE Q+V L  + L   ++  +      +LLLDE    LD  +++AL R+++ +
Sbjct: 122 STNQLSGGEWQRVRLAAVVL---QITPDANPAGQLLLLDEPMNSLDVAQQSALDRLLSAL 178

Query: 342 ---GSQIFMTGTD 351
              G  I M+  D
Sbjct: 179 CQQGLAIVMSSHD 191


>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 = 30.5 bits (69), Expect = 0.84
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 9/61 (14%)

Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGS 343
               S G+++ V +   LA             ILLLDE +A LD   R  L  ++  + +
Sbjct: 132 PFTLSGGQKQRVAIAGVLAMD---------PDILLLDEPTAGLDPAGRRELLELLKKLKA 182

Query: 344 Q 344
           +
Sbjct: 183 E 183


>gnl|CDD|36180 KOG0962, KOG0962, KOG0962, DNA repair protein RAD50, ABC-type
          ATPase/SMC superfamily [Replication, recombination and
          repair].
          Length = 1294

 Score = 29.9 bits (67), Expect = 1.1
 Identities = 16/53 (30%), Positives = 27/53 (50%)

Query: 1  MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPG 53
          M++  K+    I  F +     + F +  T+ VG NG GKT I+E + + + G
Sbjct: 1  MSSIDKLSIRGIRSFDDKDRNTIEFFSPLTLIVGANGTGKTTIIECLKYATTG 53


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

 Score = 29.7 bits (67), Expect = 1.3
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 15/94 (15%)

Query: 251 LFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNT 310
           L D + M   +R  L        +    D    +   S  ++++V +   L+        
Sbjct: 116 LIDRKAMRRRARELL------ARLGLDIDPDTLVGDLSIAQRQMVEIARALSFD------ 163

Query: 311 TGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQ 344
              A +L+LDE +A L   +   LF ++  + +Q
Sbjct: 164 ---ARVLILDEPTAALTVKETERLFDLIRRLKAQ 194


>gnl|CDD|177026 CHL00094, dnaK, heat shock protein 70.
          Length = 621

 Score = 29.7 bits (67), Expect = 1.4
 Identities = 16/48 (33%), Positives = 24/48 (50%)

Query: 181 SWCSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSL 228
           S C   E Q+ EL  KI+  + E I  L   + + +Q +N+  IK  L
Sbjct: 536 SLCYQAEKQLKELKDKISEEKKEKIENLIKKLRQALQNDNYESIKSLL 583


>gnl|CDD|73057 cd03298, ABC_ThiQ_thiamine_transporter, ABC-type thiamine tranport
           system; part of the binding-protein-dependent transport
           system tbpA-thiPQ for thiamine and TPP.  Probably
           responsible for the translocation of thiamine across the
           membrane. 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 = 211

 Score = 29.5 bits (66), Expect = 1.4
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 315 PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348
           P+LLLDE  A LD   R  +  +V D+ ++  MT
Sbjct: 148 PVLLLDEPFAALDPALRAEMLDLVLDLHAETKMT 181


>gnl|CDD|31298 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
          component [General function prediction only].
          Length = 263

 Score = 29.5 bits (66), Expect = 1.5
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 24 VFDAQHTIFVGDNGVGKTNILEAIS-FLSPGRGFRRASYADVTRIGSPSFFSTFARV 79
          + +      +G NG GK+ +L AI+  L P  G       DVT+       +  ARV
Sbjct: 29 IAEGDFVTVIGSNGAGKSTLLNAIAGDLKPTSGQILIDGVDVTKKSVAKRANLLARV 85


>gnl|CDD|133250 cd00154, Rab, Rab family.  Rab GTPases form the largest family
          within the Ras superfamily.  There are at least 60 Rab
          genes in the human genome, and a number of Rab GTPases
          are conserved from yeast to humans. Rab GTPases are
          small, monomeric proteins that function as molecular
          switches to regulate vesicle trafficking pathways.  The
          different Rab GTPases are localized to the cytosolic
          face of specific intracellular membranes, where they
          regulate distinct steps in membrane traffic pathways.
          In the GTP-bound form, Rab GTPases recruit specific
          sets of effector proteins onto membranes. Through their
          effectors, Rab GTPases regulate vesicle formation,
          actin- and tubulin-dependent vesicle movement, and
          membrane fusion.  GTPase activating proteins (GAPs)
          interact with GTP-bound Rab and accelerate the
          hydrolysis of GTP to GDP. Guanine nucleotide exchange
          factors (GEFs) interact with GDP-bound Rabs to promote
          the formation of the GTP-bound state.  Rabs are further
          regulated by guanine nucleotide dissociation inhibitors
          (GDIs), which mask C-terminal lipid binding and promote
          cytosolic localization.  While most unicellular
          organisms possess 5-20 Rab members, several have been
          found to possess 60 or more Rabs; for many of these Rab
          isoforms, homologous proteins are not found in other
          organisms.  Most Rab GTPases contain a lipid
          modification site at the C-terminus, with sequence
          motifs CC, CXC, or CCX. Lipid binding is essential for
          membrane attachment, a key feature of most Rab
          proteins.  Since crystal structures often lack
          C-terminal residues, the lipid modification site is not
          available for annotation in many of the CDs in the
          hierarchy, but is included where possible.
          Length = 159

 Score = 29.4 bits (67), Expect = 1.6
 Identities = 8/14 (57%), Positives = 13/14 (92%)

Query: 31 IFVGDNGVGKTNIL 44
          + +GD+GVGKT++L
Sbjct: 4  VLIGDSGVGKTSLL 17


>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette
           transporter (Pat) is involved in the import of very
           long-chain fatty acids (VLCFA) into the peroxisome.  The
           peroxisomal membrane forms a permeability barrier for a
           wide variety of metabolites required for and formed
           during fatty acid beta-oxidation.  To communicate with
           the cytoplasm and mitochondria, peroxisomes need
           dedicated proteins to transport such hydrophilic
           molecules across their membranes.  X-linked
           adrenoleukodystrophy (X-ALD) is caused by mutations in
           the ALD gene, which encodes ALDP (adrenoleukodystrophy
           protein ), a peroxisomal integral membrane protein that
           is a member of the ATP-binding cassette (ABC)
           transporter protein family.  The disease is
           characterized by a striking and unpredictable variation
           in phenotypic expression.  Phenotypes include the
           rapidly progressive childhood cerebral form (CCALD), the
           milder adult form, adrenomyeloneuropathy (AMN), and
           variants without neurologic involvement (i.e.
           asymptomatic)..
          Length = 166

 Score = 29.3 bits (66), Expect = 1.7
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 9/62 (14%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFM 347
           S GEQ+       LA ARL+ +   F     LDE ++ LDE+  + L++++ ++G  +  
Sbjct: 93  SGGEQQR------LAFARLLLHKPKFV---FLDEATSALDEESEDRLYQLLKELGITVIS 143

Query: 348 TG 349
            G
Sbjct: 144 VG 145


>gnl|CDD|35471 KOG0250, KOG0250, KOG0250, DNA repair protein RAD18 (SMC family
           protein) [Replication, recombination and repair].
          Length = 1074

 Score = 29.1 bits (65), Expect = 2.0
 Identities = 36/153 (23%), Positives = 66/153 (43%), Gaps = 25/153 (16%)

Query: 6   KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGF---RRASYA 62
           KI+ ++++ F  +++L + F  +    VG+NG GK+ IL A++    GR     R +S  
Sbjct: 41  KIESIHLTNFMCHSNLLIEFGPRVNFIVGNNGSGKSAILTALTLGLGGRASATNRGSSLK 100

Query: 63  DVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRI 122
           D+ + G  S              A ISI L      + +     + +I     + + +R 
Sbjct: 101 DLIKDGCSS--------------AKISITLSNSGLDAFKPEIYGNSII-----IERTIRR 141

Query: 123 SWLVPSMDRIFSGLSMERRRF-LDRMV--FAID 152
           S     + R  +G  +  ++  LD +V  F I 
Sbjct: 142 SSSTYYLLRSANGRVVSTKKEDLDTVVDHFNIQ 174


>gnl|CDD|35283 KOG0060, KOG0060, KOG0060, Long-chain acyl-CoA transporter, ABC
           superfamily (involved in peroxisome organization and
           biogenesis) [Lipid transport and metabolism, General
           function prediction only].
          Length = 659

 Score = 29.1 bits (65), Expect = 2.1
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 9/67 (13%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFM 347
           S GEQ+       LA ARL  +   FA   +LDE ++ + ED   AL+R   ++G     
Sbjct: 572 SPGEQQR------LAFARLFYHKPKFA---ILDECTSAVTEDVEGALYRKCREMGITFIS 622

Query: 348 TGTDKSV 354
            G  KS+
Sbjct: 623 VGHRKSL 629


>gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
           [General function prediction only].
          Length = 591

 Score = 29.0 bits (65), Expect = 2.2
 Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 5/42 (11%)

Query: 314 APILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355
           A + LLDE SA+LD ++R  + +++     + F+   +K+  
Sbjct: 474 ADLYLLDEPSAYLDVEQRIIVAKVI-----RRFIENNEKTAL 510


>gnl|CDD|36372 KOG1157, KOG1157, KOG1157, Predicted guanosine polyphosphate
           pyrophosphohydrolase/synthase [Signal transduction
           mechanisms].
          Length = 543

 Score = 28.9 bits (64), Expect = 2.3
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 203 EMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCALKEEYAKKLFDGRKMDSMSR 262
             I     L+     K  FP   + ++  L+  FD+   A+     +KL    K   +S 
Sbjct: 227 LGIGTNKVLLENLDFKHLFPCQHIEMSSMLEDSFDE---AMITSAIEKLEQALKKAGISY 283

Query: 263 RTLIGPHRS 271
             + G H+S
Sbjct: 284 HVIKGRHKS 292


>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
           cellular Activities) superfamily represents an ancient
           group of ATPases belonging to the ASCE (for additional
           strand, catalytic E) division of the P-loop NTPase fold.
           The ASCE division also includes ABC, RecA-like,
           VirD4-like, PilT-like, and SF1/2 helicases. Members of
           the AAA+ ATPases function as molecular chaperons, ATPase
           subunits of proteases, helicases, or nucleic-acid
           stimulated ATPases. The AAA+ proteins contain several
           distinct features in addition to the conserved
           alpha-beta-alpha core domain structure and the Walker A
           and B motifs of the P-loop NTPases..
          Length = 151

 Score = 29.0 bits (65), Expect = 2.3
 Identities = 26/158 (16%), Positives = 49/158 (31%), Gaps = 22/158 (13%)

Query: 12  ISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPS 71
           I   R    L      ++ +  G  G GKT +  AI+      G           + +  
Sbjct: 7   IEALREALELP---PPKNLLLYGPPGTGKTTLARAIANELFRPGAP------FLYLNASD 57

Query: 72  FFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDR 131
                  V  + G   + +  E  +      L         +DE++   R      ++ R
Sbjct: 58  LLEG-LVVAELFGHFLVRLLFELAEKAKPGVL--------FIDEIDSLSR--GAQNALLR 106

Query: 132 IFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGR 169
           +   L+  R    +  V      +R  + D +R +  R
Sbjct: 107 VLETLNDLRIDRENVRVIGA--TNRPLLGDLDRALYDR 142


>gnl|CDD|35286 KOG0063, KOG0063, KOG0063, RNAse L inhibitor, ABC superfamily [RNA
           processing and modification].
          Length = 592

 Score = 28.7 bits (64), Expect = 2.4
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 9/55 (16%)

Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           +   S GE + V          L       A + L+DE SA+LD ++R    +++
Sbjct: 454 VQGLSGGELQRV---------ALALCLGKPADVYLIDEPSAYLDSEQRIIASKVI 499


>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 = 28.9 bits (65), Expect = 2.4
 Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 18/105 (17%)

Query: 251 LFDGRKMDSMSRRTL---IG--PHRSDL--IVDYCDKAITIAHGSTGEQKVVLVGIFLAH 303
           L DG+ + S+S + L   I   P   +L  +    D+       S GE++ VL+      
Sbjct: 57  LLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFN--ELSGGERQRVLL------ 108

Query: 304 ARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348
           AR ++      PILLLDE ++HLD   +  L  ++  +  +   T
Sbjct: 109 ARALAQEP---PILLLDEPTSHLDIAHQIELLELLRRLARERGKT 150


>gnl|CDD|133271 cd01868, Rab11_like, Rab11-like.  Rab11a, Rab11b, and Rab25 are
          closely related, evolutionary conserved Rab proteins
          that are differentially expressed. Rab11a is
          ubiquitously synthesized, Rab11b is enriched in brain
          and heart and Rab25 is only found in epithelia.
          Rab11/25 proteins seem to regulate recycling pathways
          from endosomes to the plasma membrane and to the
          trans-Golgi network. Furthermore, Rab11a is thought to
          function in the histamine-induced fusion of
          tubulovesicles containing H+, K+ ATPase with the plasma
          membrane in gastric parietal cells and in
          insulin-stimulated insertion of GLUT4 in the plasma
          membrane of cardiomyocytes. Overexpression of Rab25 has
          recently been observed in ovarian cancer and breast
          cancer, and has been correlated with worsened outcomes
          in both diseases. In addition, Rab25 overexpression has
          also been observed in prostate cancer, transitional
          cell carcinoma of the bladder, and invasive breast
          tumor cells. GTPase activating proteins (GAPs) interact
          with GTP-bound Rab and accelerate the hydrolysis of GTP
          to GDP. Guanine nucleotide exchange factors (GEFs)
          interact with GDP-bound Rabs to promote the formation
          of the GTP-bound state.  Rabs are further regulated by
          guanine nucleotide dissociation inhibitors (GDIs),
          which facilitate Rab recycling by masking C-terminal
          lipid binding and promoting cytosolic localization. 
          Most Rab GTPases contain a lipid modification site at
          the C-terminus, with sequence motifs CC, CXC, or CCX.
          Lipid binding is essential for membrane attachment, a
          key feature of most Rab proteins.  Due to the presence
          of truncated sequences in this CD, the lipid
          modification site is not available for annotation.
          Length = 165

 Score = 28.7 bits (65), Expect = 2.6
 Identities = 8/14 (57%), Positives = 13/14 (92%)

Query: 31 IFVGDNGVGKTNIL 44
          + +GD+GVGK+N+L
Sbjct: 7  VLIGDSGVGKSNLL 20


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

 Score = 28.7 bits (64), Expect = 2.7
 Identities = 13/34 (38%), Positives = 19/34 (55%)

Query: 315 PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348
           PILLLDE  + LD   R  +  +V+ +  +  MT
Sbjct: 149 PILLLDEPFSALDPALRAEMLALVSQLCDERKMT 182


>gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
           systems, ATPase components [Inorganic ion transport and
           metabolism / Coenzyme metabolism].
          Length = 258

 Score = 28.6 bits (64), Expect = 3.0
 Identities = 30/133 (22%), Positives = 48/133 (36%), Gaps = 9/133 (6%)

Query: 28  QHTIFVGDNGVGKTNILEAIS-FLSPGRGFRRASYADVTRIGSPSFFSTFARV----EGM 82
           + T  +G NG GK+ +L+ ++  L P  G       D+  +         A V       
Sbjct: 29  EITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIASLSPKELAKKLAYVPQSPSAP 88

Query: 83  EGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSM-ERR 141
            GL    + L  R        + +     +V+E  + L +  L    DR    LS  ER+
Sbjct: 89  FGLTVYELVLLGRYPHLGLFGRPSKEDEEIVEEALELLGLEHLA---DRPVDELSGGERQ 145

Query: 142 RFLDRMVFAIDPR 154
           R L     A +  
Sbjct: 146 RVLIARALAQETP 158



 Score = 28.6 bits (64), Expect = 3.1
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 11/67 (16%)

Query: 283 TIAHGSTGEQKVVLVGIFLAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341
            +   S GE++ VL+      AR L   T    PILLLDE ++HLD   +  +  ++ D+
Sbjct: 135 PVDELSGGERQRVLI------ARALAQET----PILLLDEPTSHLDIAHQIEVLELLRDL 184

Query: 342 GSQIFMT 348
             +  +T
Sbjct: 185 NREKGLT 191


>gnl|CDD|35285 KOG0062, KOG0062, KOG0062, ATPase component of ABC transporters
           with duplicated ATPase domains/Translation elongation
           factor EF-3b [Amino acid transport and metabolism,
           Translation, ribosomal structure and biogenesis].
          Length = 582

 Score = 28.7 bits (64), Expect = 3.0
 Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 10/71 (14%)

Query: 289 TGEQKVVLVGIFLAHARLISNTTGFAP-ILLLDEISAHLDEDKRNALFRIVTDIGSQIFM 347
           +G QK  +           +  T   P +L+LDE + HLD D   AL + + +    + +
Sbjct: 484 SGGQKSRVA---------FAACTWNNPHLLVLDEPTNHLDRDSLGALAKALKNFNGGVVL 534

Query: 348 TGTDKSVFDSL 358
              D+    SL
Sbjct: 535 VSHDEEFISSL 545



 Score = 28.4 bits (63), Expect = 3.0
 Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)

Query: 17  NYASLRLVFDAQHTIFVGDNGVGKTNILEAIS 48
           N A+L L    ++ + VG NG+GK+ +L AI+
Sbjct: 97  NKANLTLSRGRRYGL-VGRNGIGKSTLLRAIA 127


>gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 591

 Score = 28.7 bits (64), Expect = 3.1
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 314 APILLLDEISAHLDEDKRNALFRIVTD 340
           APILLLDE ++ LD +    +  ++ D
Sbjct: 506 APILLLDEATSALDSETEREILDMIMD 532


>gnl|CDD|73022 cd03263, ABC_subfamily_A, The ABCA subfamily mediates the transport
           of a variety of lipid compounds.  Mutations of members
           of ABCA subfamily are associated with human genetic
           diseases, such as, familial high-density lipoprotein
           (HDL) deficiency, neonatal surfactant deficiency,
           degenerative retinopathies, and congenital
           keratinization disorders.  The ABCA1 protein is involved
           in disorders of cholesterol transport and high-density
           lipoprotein (HDL) biosynthesis.  The ABCA4 (ABCR)
           protein transports vitamin A derivatives in the outer
           segments of photoreceptor cells, and therefore, performs
           a crucial step in the visual cycle.  The ABCA genes are
           not present in yeast.  However, evolutionary studies of
           ABCA genes indicate that they arose as transporters that
           subsequently duplicated and that certain sets of ABCA
           genes were lost in different eukaryotic lineages..
          Length = 220

 Score = 28.6 bits (64), Expect = 3.3
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 310 TTGFAPILLLDEISAHLDEDKRNALFRIVTDI--GSQIFMT 348
             G   +LLLDE ++ LD   R A++ ++ ++  G  I +T
Sbjct: 148 LIGGPSVLLLDEPTSGLDPASRRAIWDLILEVRKGRSIILT 188


>gnl|CDD|35442 KOG0221, KOG0221, KOG0221, Mismatch repair ATPase MSH5 (MutS
           family) [Replication, recombination and repair].
          Length = 849

 Score = 28.1 bits (62), Expect = 3.7
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 336 RIVTDIGSQIFMTGTDKSVFDSLNETAKFMRISNHQALCI 375
           RI T I S   ++    +    LN+ AK +R +  Q+L +
Sbjct: 644 RIFTRIHSCESVSLGQSTFMIDLNQVAKALRNATAQSLVL 683


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

 Score = 28.2 bits (63), Expect = 3.7
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 12/75 (16%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI---GSQ 344
           S GEQ+ V      A AR I N      +LL DE + +LD D    + R+  +I   G+ 
Sbjct: 139 SGGEQQRV------AIARAIVNQ---PAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTT 189

Query: 345 IFMTGTDKSVFDSLN 359
           + M   D  + + + 
Sbjct: 190 VLMATHDLELVNRMR 204


>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 = 28.2 bits (63), Expect = 4.0
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 1/29 (3%)

Query: 28  QHTIFVGDNGVGKTNILEAIS-FLSPGRG 55
           Q T  VG +G GK+ +L  +  FL+P +G
Sbjct: 348 QLTALVGASGAGKSTLLNLLLGFLAPTQG 376


>gnl|CDD|33903 COG4152, COG4152, ABC-type uncharacterized transport system, ATPase
           component [General function prediction only].
          Length = 300

 Score = 27.9 bits (62), Expect = 4.3
 Identities = 40/169 (23%), Positives = 56/169 (33%), Gaps = 40/169 (23%)

Query: 32  FVGDNGVGKTNILEAI-SFLSPGRGF-----RRASYADVTRIG-------------SPSF 72
            +G NG GKT     I   L P  G         S     RIG                 
Sbjct: 33  LLGPNGAGKTTTFRMILGLLEPTEGEITWNGGPLSQEIKNRIGYLPEERGLYPKMTVEDQ 92

Query: 73  FSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNK--HLRISWLV---- 126
               A ++GM   A+I  KL+   +R    L+I     + + EL+K    +I ++     
Sbjct: 93  LKYLAELKGMP-KAEIQKKLQAWLER----LEIVGKKTKKIKELSKGNQQKIQFISAVIH 147

Query: 127 -PS---MDRIFSGLSMERRRFLDRMVFAIDPR------HRRRMIDFERL 165
            P    +D  FSGL       L   +F +            RM   E L
Sbjct: 148 EPELLILDEPFSGLDPVNVELLKDAIFELKEEGATIIFSSHRMEHVEEL 196


>gnl|CDD|36004 KOG0785, KOG0785, KOG0785, Isocitrate dehydrogenase, alpha subunit
           [Amino acid transport and metabolism].
          Length = 365

 Score = 28.0 bits (62), Expect = 4.6
 Identities = 9/43 (20%), Positives = 21/43 (48%)

Query: 233 DGKFDQSFCALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIV 275
           DG F +    + ++Y    F+ + +D+   + +  P   D++V
Sbjct: 212 DGLFLECCREVAKKYPDIKFEEQYLDTCCLKLVRNPSCFDVLV 254


>gnl|CDD|73058 cd03299, ABC_ModC_like, Archeal protein closely related to ModC. 
          ModC is an ABC-type transporter and the ATPase
          component of a molybdate transport system that also
          includes the periplasmic binding protein ModA and the
          membrane protein ModB.  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 = 235

 Score = 27.9 bits (62), Expect = 4.7
 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 24 VFDAQHTIFVGDNGVGKTNILEAIS-FLSPGRGFRRASYADVT 65
          V    + + +G  G GK+ +LE I+ F+ P  G    +  D+T
Sbjct: 22 VERGDYFVILGPTGSGKSVLLETIAGFIKPDSGKILLNGKDIT 64


>gnl|CDD|31318 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
           [Inorganic ion transport and metabolism].
          Length = 254

 Score = 27.9 bits (62), Expect = 4.8
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 11/68 (16%)

Query: 274 IVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNA 333
           + D  D+   I   S G+++ V     LA A L  N      +LLLDE    +D   +  
Sbjct: 129 MEDLRDR--QIGELSGGQKQRV----LLARA-LAQN----PDLLLLDEPFTGVDVAGQKE 177

Query: 334 LFRIVTDI 341
           ++ ++ ++
Sbjct: 178 IYDLLKEL 185


>gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction
           only].
          Length = 301

 Score = 27.9 bits (62), Expect = 5.2
 Identities = 9/40 (22%), Positives = 20/40 (50%)

Query: 9   FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS 48
           F++         L  +   + T+ +G +GVGK+ ++ A+ 
Sbjct: 146 FVSAKNGDGLEELAELLAGKITVLLGQSGVGKSTLINALL 185


>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 = 27.7 bits (62), Expect = 5.3
 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 5/42 (11%)

Query: 301 LAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341
           +A AR L+ +     PIL+LDE ++ LD +    +   +  +
Sbjct: 105 IAIARALLRD----PPILILDEATSALDPETEALILEALRAL 142


>gnl|CDD|73038 cd03279, ABC_sbcCD, SbcCD and other Mre11/Rad50 (MR) complexes
          are implicated in the metabolism of DNA ends. They
          cleave ends sealed by hairpin structures and are
          thought to play a role in removing protein bound to DNA
          termini..
          Length = 213

 Score = 27.5 bits (61), Expect = 5.7
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 5  IKIKFLNISEFRNYASLRLVFDAQHTIFV--GDNGVGKTNILEAISF 49
          +K++  N   FR    +       + +F+  G  G GK+ IL+AI++
Sbjct: 4  LKLELKNFGPFREEQVIDFTGLDNNGLFLICGPTGAGKSTILDAITY 50


>gnl|CDD|72996 cd03237, ABC_RNaseL_inhibitor_domain2, The ATPase domain 2 of RNase
           L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI),
           is a key enzyme in ribosomal biogenesis, formation of
           translation preinitiation complexes, and assembly of HIV
           capsids.  RLI's are not transport proteins and thus
           cluster with a group of soluble proteins that lack the
           transmembrane components commonly found in other members
           of the family.  Structurally, RLI's have an N-terminal
           Fe-S domain and two nucleotide-binding domains which are
           arranged to form two composite active sites in their
           interface cleft.  RLI is one of the most conserved
           enzymes between archaea and eukaryotes with a sequence
           identity of more than 48%.  The high degree of
           evolutionary conservation suggests that RLI performs a
           central role in archaeal and eukaryotic physiology..
          Length = 246

 Score = 27.6 bits (61), Expect = 6.3
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 314 APILLLDEISAHLDEDKRNALFRIV 338
           A I LLDE SA+LD ++R    +++
Sbjct: 134 ADIYLLDEPSAYLDVEQRLMASKVI 158


>gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. 
          Length = 161

 Score = 27.5 bits (62), Expect = 6.7
 Identities = 8/39 (20%), Positives = 19/39 (48%)

Query: 9  FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47
           ++         L+ +   + ++  G +GVGK+ +L A+
Sbjct: 17 VVSAKTGEGIEELKPLLKGKTSVLAGQSGVGKSTLLNAL 55


>gnl|CDD|39094 KOG3891, KOG3891, KOG3891, Secretory vesicle-associated protein
           ICA69, contains Arfaptin domain [Signal transduction
           mechanisms, Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 436

 Score = 27.4 bits (60), Expect = 6.8
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 248 AKKLFDGRKMDSMSRRTLIGPHRSDLI 274
           AK+ FD  KMD   +  L+G  R +L+
Sbjct: 197 AKENFDKLKMDVCQKVDLLGASRCNLL 223


>gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC.  YjeQ (YloQ in Bacillus subtilis)
           represents a protein family whose members are broadly
           conserved in bacteria and have been shown to be
           essential to the growth of E. coli and B. subtilis.
           Proteins of the YjeQ family contain all sequence motifs
           typical of the vast class of P-loop-containing GTPases,
           but show a circular permutation, with a G4-G1-G3 pattern
           of motifs as opposed to the regular G1-G3-G4 pattern
           seen in most GTPases. All YjeQ family proteins display a
           unique domain architecture, which includes an N-terminal
           OB-fold RNA-binding domain, the central permuted GTPase
           domain, and a zinc knuckle-like C-terminal cysteine
           domain. This domain architecture suggests a role for
           YjeQ as a regulator of translation..
          Length = 287

 Score = 27.4 bits (61), Expect = 6.9
 Identities = 9/43 (20%), Positives = 20/43 (46%)

Query: 5   IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47
             +  ++         LR     + ++ VG +GVGK+ ++ A+
Sbjct: 139 YPVLAVSAKTGEGLDELREYLKGKTSVLVGQSGVGKSTLINAL 181


>gnl|CDD|37542 KOG2331, KOG2331, KOG2331, Predicted glycosylhydrolase [General
           function prediction only].
          Length = 526

 Score = 27.3 bits (60), Expect = 6.9
 Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 18/92 (19%)

Query: 134 SGLSMERRRFLDRMVFAIDPRHRRRM------IDFERLMRGRNRLLTEGYFDSSWCSSIE 187
           + L ++     +   F  D  +   +            +  +N+   +   D+ W   ++
Sbjct: 372 TTLVLDGGTLTEISAFCYDSDNLTTLTITCETSLLIGHISLKNQQKMDKTGDAEW-WIVK 430

Query: 188 AQMAELGVKINIARVEMINALSSLIMEYVQKE 219
           A             VE++  LSS     V+ E
Sbjct: 431 AH-----------NVELVPGLSSSKSLTVRLE 451


>gnl|CDD|72983 cd03224, ABC_TM1139_LivF_branched, LivF (TM1139) is part of the
          LIV-I bacterial ABC-type two-component transport system
          that imports neutral, branched-chain amino acids.  The 
          E. coli branched-chain amino acid transporter comprises
          a heterodimer of ABC transporters (LivF and LivG), a
          heterodimer of six-helix TM domains (LivM and LivH),
          and one of two alternative soluble periplasmic
          substrate binding proteins (LivK or LivJ).  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..
          Length = 222

 Score = 27.3 bits (61), Expect = 7.0
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 33 VGDNGVGKTNILEAISFLSPGRG 55
          +G NG GKT +L+ I  L P R 
Sbjct: 32 LGRNGAGKTTLLKTIMGLLPPRS 54


>gnl|CDD|144183 pfam00493, MCM, MCM2/3/5 family. 
          Length = 327

 Score = 27.1 bits (61), Expect = 7.1
 Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 5/33 (15%)

Query: 29 HTIFVGDNGVGKTNILEAISFLSPGRGFRRASY 61
          + + VGD G  K+ +L+ ++ L+P     RA Y
Sbjct: 59 NVLLVGDPGTAKSQLLKYVAKLAP-----RAVY 86


>gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
           (vWA) domain [General function prediction only].
          Length = 4600

 Score = 27.4 bits (60), Expect = 7.2
 Identities = 7/24 (29%), Positives = 15/24 (62%)

Query: 28  QHTIFVGDNGVGKTNILEAISFLS 51
           + T+ VG+ G GKT +++ ++   
Sbjct: 465 EPTLLVGETGTGKTTMIQYLALKL 488


>gnl|CDD|31240 COG1038, PycA, Pyruvate carboxylase [Energy production and
            conversion].
          Length = 1149

 Score = 27.1 bits (60), Expect = 7.4
 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 10/68 (14%)

Query: 58   RASYADVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIR----VV 113
            R +Y DV+ + +P+FF       G+    +I +++E      ++   I +   +    V 
Sbjct: 994  RETYGDVSVLPTPTFFY------GLRPGEEIEVEIEKGKTLIIKLQAIGEPDEKGMRTVY 1047

Query: 114  DELNKHLR 121
             ELN   R
Sbjct: 1048 FELNGQPR 1055


>gnl|CDD|30759 COG0410, LivF, ABC-type branched-chain amino acid transport
          systems, ATPase component [Amino acid transport and
          metabolism].
          Length = 237

 Score = 27.4 bits (61), Expect = 7.4
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 33 VGDNGVGKTNILEAISFLSPGRG 55
          +G NG GKT +L+ I  L   R 
Sbjct: 35 LGRNGAGKTTLLKTIMGLVRPRS 57


>gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3  Elongation factor 3 (EF-3) is a
           cytosolic protein required by fungal ribosomes for in
           vitro protein synthesis and for in vivo growth.  EF-3
           stimulates the binding of the EF-1: GTP: aa-tRNA ternary
           complex to the ribosomal A site by facilitated release
           of the deacylated tRNA from the E site.  The reaction
           requires ATP hydrolysis.  EF-3 contains two ATP
           nucleotide binding sequence (NBS) motifs.  NBSI is
           sufficient for the intrinsic ATPase activity. NBSII is
           essential for the ribosome-stimulated functions..
          Length = 144

 Score = 27.3 bits (61), Expect = 7.4
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 11/48 (22%)

Query: 288 STGEQ-KVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334
           S GE+ ++ L  + L +            +LLLDE + HLD +   AL
Sbjct: 72  SGGEKMRLALAKLLLENP----------NLLLLDEPTNHLDLESIEAL 109


>gnl|CDD|173865 cd08500, PBP2_NikA_DppA_OppA_like_4, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 499

 Score = 27.2 bits (61), Expect = 7.9
 Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 7/37 (18%)

Query: 318 LLDEISAHLDEDKRNALF----RIVTDIGSQIFMTGT 350
           L D+ +  LD++KR AL+    +I  +    + + GT
Sbjct: 450 LYDKGAVELDQEKRKALYAEIQKIAAE---NLPVIGT 483


>gnl|CDD|147747 pfam05762, VWA_CoxE, VWA domain containing CoxE-like protein.  This
           family is annotated by SMART as containing a VWA type
           domain. The exact function of this family is unknown. It
           is found as part of a CO oxidising (Cox) system operon
           is several bacteria.
          Length = 223

 Score = 27.0 bits (60), Expect = 7.9
 Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 8/43 (18%)

Query: 125 LVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMR 167
           L  ++  +  GL+  RRR           R R   ID  R +R
Sbjct: 1   LARALAALLLGLARRRRRRK--------RRRRGGRIDLRRTLR 35


>gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins
           (PDR1-15), ABC superfamily [Secondary metabolites
           biosynthesis, transport and catabolism].
          Length = 1391

 Score = 27.1 bits (60), Expect = 8.0
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 30  TIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGMEGLADIS 89
           T  +G++G GKT +L+ ++    GR        D+   G P    TFARV G     DI 
Sbjct: 820 TALMGESGAGKTTLLDVLA----GRKTGGYIEGDILISGFPKDQETFARVSGYVEQQDIH 875

Query: 90  IKLET 94
               T
Sbjct: 876 SPELT 880


>gnl|CDD|34390 COG4778, PhnL, ABC-type phosphonate transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 235

 Score = 27.2 bits (60), Expect = 8.6
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 315 PILLLDEISAHLDEDKRNALFRIV 338
           PILLLDE +A LD   R  +  ++
Sbjct: 172 PILLLDEPTASLDATNRAVVVELI 195


>gnl|CDD|33889 COG4133, CcmA, ABC-type transport system involved in cytochrome c
           biogenesis, ATPase component [Posttranslational
           modification, protein turnover, chaperones].
          Length = 209

 Score = 27.2 bits (60), Expect = 8.8
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 9/52 (17%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVT 339
           S G+Q+ V      A ARL       AP+ +LDE    LD++    L  ++ 
Sbjct: 132 SAGQQRRV------ALARLW---LSPAPLWILDEPFTALDKEGVALLTALMA 174


>gnl|CDD|173868 cd08503, PBP2_NikA_DppA_OppA_like_17, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 460

 Score = 26.8 bits (60), Expect = 9.3
 Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 4/32 (12%)

Query: 318 LLDEISAHLDEDKRNALF----RIVTDIGSQI 345
           LLD   A LDE KR  L+    +I+ D G  I
Sbjct: 411 LLDAARAELDEAKRKELYAEMQQILHDEGGII 442


>gnl|CDD|72994 cd03235, ABC_Metallic_Cations, ABC component of the metal-type
           transporters.  This family includes transporters
           involved in the uptake of various metallic cations such
           as iron, manganese, and zinc.  The ATPases of this group
           of transporters are very similar to members of
           iron-siderophore uptake family suggesting that they
           share a common ancestor.  The best characterized
           metal-type ABC transporters are the YfeABCD system of Y.
           pestis, the SitABCD system of Salmonella enterica
           serovar Typhimurium, and the SitABCD transporter of
           Shigella flexneri.  Moreover other uncharacterized
           homologs of these metal-type transporters are mainly
           found in pathogens like Haemophilus or enteroinvasive E.
           coli isolates..
          Length = 213

 Score = 27.0 bits (60), Expect = 9.3
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 9/55 (16%)

Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           I   S G+Q+ V     LA A L+ +      +LLLDE  A +D   +  ++ ++
Sbjct: 130 IGELSGGQQQRV----LLARA-LVQD----PDLLLLDEPFAGVDPKTQEDIYELL 175


>gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease
           PIM1/LON [Posttranslational modification, protein
           turnover, chaperones].
          Length = 906

 Score = 26.8 bits (59), Expect = 9.4
 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)

Query: 32  FVGDNGVGKTNILEAISFLSPGRGFRRASYADVT 65
           FVG  GVGKT+I ++I+  +  R F R S   +T
Sbjct: 443 FVGPPGVGKTSIAKSIA-RALNRKFFRFSVGGMT 475


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

 Score = 27.0 bits (60), Expect = 9.6
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 9/54 (16%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341
           S G+Q+ V      A AR + N      I+L DE + +LD      +  ++ ++
Sbjct: 144 SGGQQQRV------AIARALINN---PKIILADEPTGNLDSKTAKEVLELLREL 188


>gnl|CDD|133292 cd01892, Miro2, Miro2 subfamily.  Miro (mitochondrial Rho) proteins
           have tandem GTP-binding domains separated by a linker
           region containing putative calcium-binding EF hand
           motifs.  Genes encoding Miro-like proteins were found in
           several eukaryotic organisms.  This CD represents the
           putative GTPase domain in the C terminus of Miro
           proteins.  These atypical Rho GTPases have roles in
           mitochondrial homeostasis and apoptosis.  Most Rho
           proteins contain a lipid modification site at the
           C-terminus; however, Miro is one of few Rho subfamilies
           that lack this feature.
          Length = 169

 Score = 26.8 bits (60), Expect = 9.7
 Identities = 25/92 (27%), Positives = 33/92 (35%), Gaps = 25/92 (27%)

Query: 33  VGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFA----RVEGMEG---L 85
           +G  G GK+ +L A  FL  GR F   +Y       SP+    +A     V G E    L
Sbjct: 10  LGAKGSGKSALLRA--FL--GRSFSLNAY-------SPTIKPRYAVNTVEVYGQEKYLIL 58

Query: 86  ADISIKLE---TRDDRSVRCLQINDVVIRVVD 114
            ++          D     C    DV   V D
Sbjct: 59  REVGEDEVAILLNDAELAAC----DVACLVYD 86


>gnl|CDD|73048 cd03289, ABCC_CFTR2, The CFTR subfamily domain 2.  The cystic
           fibrosis transmembrane regulator (CFTR), the product of
           the gene mutated in patients with cystic fibrosis, has
           adapted the ABC transporter structural motif to form a
           tightly regulated anion channel at the apical surface of
           many epithelia.  Use of the term assembly of a
           functional ion channel implies the coming together of
           subunits or at least smaller not-yet functional
           components of the active whole.  In fact, on the basis
           of current knowledge only the CFTR polypeptide itself is
           required to form an ATP- and protein kinase A-dependent
           low-conductance chloride channel of the type present in
           the apical membrane of many epithelial cells.  CFTR
           displays the typical organization (IM-ABC)2 and carries
           a characteristic hydrophilic R-domain that separates
           IM1-ABC1 from IM2-ABC2..
          Length = 275

 Score = 26.9 bits (59), Expect = 9.8
 Identities = 12/14 (85%), Positives = 12/14 (85%)

Query: 314 APILLLDEISAHLD 327
           A ILLLDE SAHLD
Sbjct: 157 AKILLLDEPSAHLD 170


>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
           ATPase domains [General function prediction only].
          Length = 530

 Score = 26.8 bits (59), Expect = 9.9
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 9/47 (19%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334
           S G ++ V     LA A L+        +LLLDE + HLD +    L
Sbjct: 155 SGGWRRRVA----LARA-LLEE----PDLLLLDEPTNHLDLESIEWL 192


>gnl|CDD|153337 cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and
           Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein
           4 and similar proteins.  F-BAR domains are dimerization
           modules that bind and bend membranes and are found in
           proteins involved in membrane dynamics and actin
           reorganization. This subfamily is composed of
           Cdc42-Interacting Protein 4 (CIP4), Formin Binding
           Protein 17 (FBP17), FormiN Binding Protein 1-Like
           (FNBP1L), and similar proteins. CIP4 and FNBP1L are
           Cdc42 effectors that bind Wiskott-Aldrich syndrome
           protein (WASP) and function in endocytosis. CIP4 and
           FBP17 bind to the Fas ligand and may be implicated in
           the inflammatory response. CIP4 may also play a role in
           phagocytosis. Members of this subfamily typically
           contain an N-terminal F-BAR domain and a C-terminal SH3
           domain. In addition, some members such as FNBP1L contain
           a central Cdc42-binding HR1 domain. F-BAR domains form
           banana-shaped dimers with a positively-charged concave
           surface that binds to negatively-charged lipid
           membranes. They can induce membrane deformation in the
           form of long tubules.
          Length = 251

 Score = 26.8 bits (60), Expect = 10.0
 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 2/24 (8%)

Query: 230 GFLD--GKFDQSFCALKEEYAKKL 251
            FL+  GKF +   A+++EYAKKL
Sbjct: 19  DFLERYGKFVKERAAIEQEYAKKL 42


  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
   0.326    0.139    0.402 

Gapped
Lambda     K      H
   0.267   0.0696    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,503,495
Number of extensions: 247431
Number of successful extensions: 1174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1165
Number of HSP's successfully gapped: 140
Length of query: 375
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 280
Effective length of database: 4,210,882
Effective search space: 1179046960
Effective search space used: 1179046960
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: 58 (26.2 bits)