RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780901|ref|YP_003065314.1| single-stranded-DNA-specific
exonuclease protein [Candidatus Liberibacter asiaticus str. psy62]
         (600 letters)



>gnl|CDD|30953 COG0608, RecJ, Single-stranded DNA-specific exonuclease [DNA
           replication, recombination, and repair].
          Length = 491

 Score =  365 bits (939), Expect = e-101
 Identities = 182/492 (36%), Positives = 262/492 (53%), Gaps = 23/492 (4%)

Query: 68  LMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI 127
           L+ DP +L D +KAA RI +AI   EKI+I+GDYD DG  S A++ + L     + + YI
Sbjct: 12  LLLDPFLLKDMEKAAARIAEAIEKGEKILIYGDYDADGITSAAILAKALRRLGADVDYYI 71

Query: 128 PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSE 187
           P+R  +GYG     + K   EGA LIITVD GS S + +  A   GIDVIV DHH    E
Sbjct: 72  PNRFEEGYG----AIRKLKEEGADLIITVDNGSGSLEEIARAKELGIDVIVTDHHPPGEE 127

Query: 188 EIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVAL 247
              A A+VNPN          L   GV F +   +   LR+D           LLDLVAL
Sbjct: 128 LPDAVAIVNPNLPGCDYPFKELAGVGVAFKLARALLEELRKD-----------LLDLVAL 176

Query: 248 ATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISS-PITAENLGYMIGPSIN 306
            TV DV PL G NR  V +GL   R+ G PG+KAL++     +   TA ++G++IGP IN
Sbjct: 177 GTVADVQPLTGENRILVNQGLKRLRKSGRPGIKALLKLAGRDTRQPTASDIGFIIGPRIN 236

Query: 307 AGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQ 366
           A GR+G++  G  LL+++D ++ E LA +L++LN+ R+ +E+ +L++A   V     +  
Sbjct: 237 AAGRLGDAKAGVELLLTEDDEKAESLAEELELLNEERKKIENELLKEAIKIVEAL--EES 294

Query: 367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIE-GFDIGKMV 425
              VIVV  + WHPG++G++A+RL   FGRP   ++ + +G   GS RSI  G D+ K++
Sbjct: 295 GEYVIVVSEEEWHPGVLGIVASRLLNAFGRPVIVLAGDAEGGAKGSARSIAKGIDLRKLL 354

Query: 426 SFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNA 485
                + +L K GGHAMAAGL+++  N         + A  I+         +ID  L  
Sbjct: 355 RKGRSKLLLEKFGGHAMAAGLSLKEENLEEFRGILGEIASMILDKEELREKLEIDFALKD 414

Query: 486 SAVNIALIDMLESAGPYGAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQDSETLQAIA 545
             + + L+  LE+  P+G GNP P+F     ++   R     HL+    +     L AI 
Sbjct: 415 EDITLELVSALETLEPFGQGNPLPLFLRKAAEVVGGRGG--GHLKAAGANIPK--LDAIE 470

Query: 546 FRVYGTPLGEFL 557
           F      L    
Sbjct: 471 FLKDLDKLLGEQ 482


>gnl|CDD|144819 pfam01368, DHH, DHH family.  It is predicted that this family of
           proteins all perform a phosphoesterase function. It
           included the single stranded DNA exonuclease RecJ.
          Length = 156

 Score =  130 bits (330), Expect = 7e-31
 Identities = 57/169 (33%), Positives = 82/169 (48%), Gaps = 19/169 (11%)

Query: 88  AIYNSEKIMIFGDY--DVDGAASVALMMRFLSHCSVNANMYIPDRIVDG--YGPNPSLME 143
           AI   EKI+I G Y  D DG  S A +   L       +  +P R ++G  YG +  ++E
Sbjct: 1   AIKEGEKILIVGHYNPDADGIGSAAALALALKRLGAEKDYVVPPREIEGKFYGLSDEIVE 60

Query: 144 KFINEG--AQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLD 201
               E   A L+ITVD GST+ + ++ A   GIDVIVIDHH+    ++P    +NP    
Sbjct: 61  DIAEEKGKADLLITVDTGSTAREEIELAKLLGIDVIVIDHHEPPENDLPPI--INPA--- 115

Query: 202 DLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATV 250
           DL     L A+    LV   +  +  + N+        +L DL+AL  V
Sbjct: 116 DLGPYIDLSASSTAELVAEALLGLELKLNR--------NLADLLALGIV 156


>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
           DnaJ-type Zn finger domain [DNA replication,
           recombination, and repair].
          Length = 715

 Score = 49.9 bits (119), Expect = 2e-06
 Identities = 42/160 (26%), Positives = 63/160 (39%), Gaps = 25/160 (15%)

Query: 63  PSIRLLMPDPLILT----DCDKAARRIVQAIYNSEKIMIFGDYDVDG-AASVALMMRFL- 116
           P+    + D  +L     D    A+ I +A+     I+I    D DG  A VAL    L 
Sbjct: 310 PADVGFLVDSEVLEALKPDMVDVAKEIRRAVLEGRPIIIRHHADADGYCAGVALEKAILP 369

Query: 117 ----SHCSVNANMYIPDR---------IVDGYGPNPSLMEKFINEGAQ--LIITVDCGST 161
                H   +A  ++  R         + D        +E     G +  L++ VD GST
Sbjct: 370 LIEDVHPDEDAEYHLFKRRPSKAPFYELEDVTRDLNFALEDAHRHGQKLPLLVLVDNGST 429

Query: 162 SYD--ALQYATNQGIDVIVIDHHQVKSEEIPAY--ALVNP 197
             D  A++     GID++V+DHH      +  Y    VNP
Sbjct: 430 EEDIPAIKQLKAYGIDIVVVDHHYPDEAVVDEYVDVHVNP 469


>gnl|CDD|145431 pfam02272, DHHA1, DHHA1 domain.  This domain is often found
           adjacent to the DHH domain pfam01368 and is called DHHA1
           for DHH associated domain. This domain is diagnostic of
           DHH subfamily 1 members. This domains is also found in
           alanyl tRNA synthetase, suggesting that this domain may
           have an RNA binding function. The domain is about 60
           residues long and contains a conserved GG motif.
          Length = 69

 Score = 45.7 bits (109), Expect = 3e-05
 Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 396 RPSFAISFEEDGKGIGSGRSIEGFDI-GKMVSFAVEEGILVKGGGHAMAAGLTVE 449
           +P    + EEDGK   S RS +G D+ G  +   V E +   GGGH  AAG   +
Sbjct: 2   KPVVLFA-EEDGKVKVSARSSKGLDVKGGELLKEVAEILGGGGGGHPDAAGAGGK 55


>gnl|CDD|30963 COG0618, COG0618, Exopolyphosphatase-related proteins [General
           function prediction only].
          Length = 332

 Score = 45.0 bits (106), Expect = 5e-05
 Identities = 24/127 (18%), Positives = 44/127 (34%), Gaps = 10/127 (7%)

Query: 83  RRIVQAIYNSEKIMIFG--DYDVDGAASVALMMRFLSHCSVNANMYI--------PDRIV 132
             +++ I   +KI+I    + D D   S   +   L     N  +              +
Sbjct: 7   AELLELIKAHDKILILTHENPDPDALGSALALAELLKDLGKNKEVLYVGPITHPENRAFL 66

Query: 133 DGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAY 192
           +  G     +E    +   L+I VD  +      Q        VIVIDHH   ++    +
Sbjct: 67  NLLGDELERIEDDPLDDYDLVIIVDTANLPRIGDQELLLDSKKVIVIDHHPGNNDIYGDF 126

Query: 193 ALVNPNR 199
             ++P+ 
Sbjct: 127 VWIDPSA 133



 Score = 28.5 bits (63), Expect = 5.0
 Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 403 FEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQK 462
            EEDG    S RS    ++ +    A + G    GGGHA+AAG  +         D  + 
Sbjct: 267 DEEDGSIRVSDRSKGIGNVNE---IAFKFG----GGGHALAAGARIPLGILESADDLLKL 319

Query: 463 F 463
            
Sbjct: 320 L 320


>gnl|CDD|145115 pfam01784, NIF3, NIF3 (NGG1p interacting factor 3).  This family
           contains several NIF3 (NGG1p interacting factor 3)
           protein homologues. NIF3 interacts with the yeast
           transcriptional coactivator NGG1p which is part of the
           ADA complex, the exact function of this interaction is
           unknown.
          Length = 238

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 131 IVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEI 189
           I  G G   SL+E+   +GA L+IT   G   +     A  +GI++I   H+   +E  
Sbjct: 175 ICGGSGS--SLIEEAKAKGADLLIT---GELKHHDALDAKEKGINLIDAGHYA--TERF 226


>gnl|CDD|33676 COG3887, COG3887, Predicted signaling protein consisting of a
           modified GGDEF domain and a DHH domain [Signal
           transduction mechanisms].
          Length = 655

 Score = 36.8 bits (85), Expect = 0.017
 Identities = 29/128 (22%), Positives = 49/128 (38%), Gaps = 19/128 (14%)

Query: 85  IVQAIYNSEKIMIFG----DYDVDGAA----SVALMMRFLSHCSVNANMYIPD--RIVDG 134
           +   I  S+ + I G    D D  G+A      A M    +   ++     PD  R ++ 
Sbjct: 330 LSDIIKESDNVFIMGHKFPDMDALGSAIGMQKFASMNNKEAFAVLDPEDMSPDVERAINE 389

Query: 135 YGPNPSLMEKFIN-EGAQ-------LIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS 186
              N     +FI    A        L++ VD    S    +   ++   V+VIDHH+ + 
Sbjct: 390 IEKNSEGKTRFITPSDAMELSTERSLLVIVDTHKPSLVLNEEFLDKFEKVVVIDHHR-RD 448

Query: 187 EEIPAYAL 194
           E+  +  L
Sbjct: 449 EDFISNPL 456


>gnl|CDD|32540 COG2404, COG2404, Predicted phosphohydrolase (DHH superfamily)
           [General function prediction only].
          Length = 339

 Score = 35.0 bits (80), Expect = 0.055
 Identities = 35/132 (26%), Positives = 50/132 (37%), Gaps = 20/132 (15%)

Query: 94  KIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGAQ 151
              I+   D+DG A  A++ RF      NAN       RI            +    G  
Sbjct: 1   VYHIYSHNDLDGYACAAVVKRFFGKNVYNANFGREVSARINSILE-----SAEESGIGDA 55

Query: 152 LIITVDCGST------SYDALQYATNQGIDVIVIDHHQVKSEEIPAYA-LVNPNRLDDLS 204
           ++I+ D            + L+ ATN+G  V  IDHH+  +E             +DD  
Sbjct: 56  ILIS-DLDVNLDRFEELVEKLKEATNKGTKVKWIDHHKTANETKEEVREAGVSVYVDD-- 112

Query: 205 GQGHLCAAGVVF 216
                CAAGVV+
Sbjct: 113 ---SRCAAGVVY 121


>gnl|CDD|143409 cd07090, ALDH_F9_TMBADH, NAD+-dependent
           4-trimethylaminobutyraldehyde dehydrogenase, ALDH family
           9A1.  NAD+-dependent, 4-trimethylaminobutyraldehyde
           dehydrogenase (TMABADH, EC=1.2.1.47), also known as
           aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in
           humans, is a cytosolic tetramer which catalyzes the
           oxidation of gamma-aminobutyraldehyde involved in
           4-aminobutyric acid (GABA) biosynthesis  and also
           oxidizes betaine aldehyde
           (gamma-trimethylaminobutyraldehyde) which is involved in
           carnitine biosynthesis.
          Length = 457

 Score = 33.8 bits (78), Expect = 0.15
 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 95  IMIFGDYDVDGAASVALMMRFLSH---CSVNANMYIPDRIVD 133
           ++IF D D++ A + A+M  FLS    CS    +++   I D
Sbjct: 231 LIIFDDADLENAVNGAMMANFLSQGQVCSNGTRVFVQRSIKD 272


>gnl|CDD|113050 pfam04263, TPK_catalytic, Thiamin pyrophosphokinase, catalytic
           domain.  Family of thiamin pyrophosphokinase
           (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses
           the transfer of a pyrophosphate group from ATP to
           vitamin B1 (thiamin) to form the coenzyme thiamin
           pyrophosphate (TPP). Thus, TPK is important for the
           formation of a coenzyme required for central metabolic
           functions. The structure of thiamin pyrophosphokinase
           suggest that the enzyme may operate by a mechanism of
           pyrophosphoryl transfer similar to those described for
           pyrophosphokinases functioning in nucleotide
           biosynthesis.
          Length = 122

 Score = 32.3 bits (74), Expect = 0.41
 Identities = 20/79 (25%), Positives = 26/79 (32%), Gaps = 12/79 (15%)

Query: 103 VDGAASVALMMRFLSHCSVNANMYIPDRIV-DGYGPNPSLMEKFINEGAQLIITVDCGST 161
            DG A+             +     PD +V D       L   +   G  LI   +   T
Sbjct: 21  ADGGANHLR----------DFLSLKPDFVVGDFDSITEELRAYYKEAGVNLIHFPEKDDT 70

Query: 162 SYD-ALQYATNQGIDVIVI 179
             + AL  A   G D IVI
Sbjct: 71  DLELALDEALELGADEIVI 89


>gnl|CDD|32480 COG2327, WcaK, Uncharacterized conserved protein [Function
           unknown].
          Length = 385

 Score = 31.5 bits (71), Expect = 0.71
 Identities = 25/109 (22%), Positives = 43/109 (39%), Gaps = 16/109 (14%)

Query: 314 SNLGSRLLISDDSQEL-EMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIV 372
           +     L+    S +L    A+   VL+    L+ S    +    +L  CD        +
Sbjct: 237 ALWRITLIDYGASDDLAVADAIAQLVLDSAEILVSSDEYAEELGGILAACD--------L 288

Query: 373 VEGDRWHPGIVGLLA