RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781193|ref|YP_003065606.1| putative DNA polymerase from
bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62]
(675 letters)
>gnl|CDD|128758 smart00482, POLAc, DNA polymerase A domain.
Length = 206
Score = 95.4 bits (238), Expect = 5e-20
Identities = 60/281 (21%), Positives = 101/281 (35%), Gaps = 85/281 (30%)
Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423
+R +A G LV AD + IE R+LA ++G++ L+AF G D++ T A+ F V +
Sbjct: 4 IRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVPEEE 63
Query: 424 VTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCR 483
VTK+ R K + + Y G A +A G++ L+K
Sbjct: 64 VTKELRRAAKAINFGIIY--GMGAK-GLAEQLGISEAEAKELIKA--------------- 105
Query: 484 WMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKR 543
P VK+ ++ + + T+ +R
Sbjct: 106 -YFARFPG--------------VKRYIKRTLEEARR------KGYVTTLFG-------RR 137
Query: 544 RDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQ 603
R +P + +N P R+ R+ +N +Q
Sbjct: 138 RYIPDI---DSRN------PVLRAA------AERAAVNA------------------PIQ 164
Query: 604 AVSRDILAEGMMNATKAGY------DIVLTVHDEIVCETPD 638
+ DIL M+ +A ++L VHDE+V E P+
Sbjct: 165 GSAADILKLAMIKMDEALKEKGLRARLLLQVHDELVFEVPE 205
>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
Provisional.
Length = 553
Score = 86.2 bits (214), Expect = 3e-17
Identities = 46/163 (28%), Positives = 65/163 (39%), Gaps = 38/163 (23%)
Query: 296 EAMNSDGRLRGTLQFLGASRTGRWSGCVFPP--QNLPRPSRSHEELDQIITHLPTSITSD 353
+ DGR G TGRW+ P Q +PR
Sbjct: 279 DYWVRDGRFHPEYVPGGVV-TGRWAS--RGPNAQQIPRD--------------------- 314
Query: 354 PDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTY 413
+RS +A G KLVVAD + IE RVLA +G++ ++AF TG DL+ T
Sbjct: 315 ----------IRSAFVADPGWKLVVADASQIELRVLAAYSGDERMIEAFRTGGDLHRLTA 364
Query: 414 ARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTG 456
+ F + K++RA+ K Y +K Q+ A G
Sbjct: 365 SVGFGKPEEE--KEERALAKAANFGAIYGATSKGLQEYAKNYG 405
Score = 28.8 bits (65), Expect = 4.1
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 595 GKLTEN-IVQAVSRDILAEGMM-----NATKAGYDIVLTVHDEIVCETPD 638
G+ T N VQ + D + A ++V VHDE+V E P+
Sbjct: 463 GRFTRNFPVQGTAADWAKLALALLRRRLAEGLDAELVFFVHDEVVVECPE 512
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 64.7 bits (159), Expect = 7e-11
Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423
+R +A EG KL+ AD + IE R+LA ++G++ ++AF GED++ T + F V +
Sbjct: 641 IRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLEE 700
Query: 424 VTKDQRAIGKVM 435
VT +QR K +
Sbjct: 701 VTSEQRRRAKAI 712
Score = 32.8 bits (76), Expect = 0.29
Identities = 32/139 (23%), Positives = 48/139 (34%), Gaps = 29/139 (20%)
Query: 57 LKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLA-------RSNGLPSAL 109
LK LE+ + V N ++ VL I + +LA R +GL S
Sbjct: 362 LKPLLEDPAIKKVGQNLKYDLHVLA---RYGIELRGIAFDTMLASYLLDPGRRHGLDSL- 417
Query: 110 KAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTR 169
A + K +E+ K T + + EA EY D VT
Sbjct: 418 -----AERYLGHKTISFEEVAG---KQLT------FAQVDLEEA----AEYAAEDADVTL 459
Query: 170 EIFKRLEPLSSKEQELWYL 188
+ + L+P +E L L
Sbjct: 460 RLHEVLKPKLLEEPGLLEL 478
>gnl|CDD|161944 TIGR00593, pola, DNA polymerase I. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University).
Length = 887
Score = 61.2 bits (149), Expect = 9e-10
Identities = 39/124 (31%), Positives = 59/124 (47%), Gaps = 9/124 (7%)
Query: 325 PPQNLPRPSRSHEELDQIITHLPTSITSDPDP-LQII------SDCVRSCVIASEGKKLV 377
P P R H +Q T T S +P LQ I +R +A +G L+
Sbjct: 604 PELVNPDTGRIHTTFNQTGT--ATGRLSSSNPNLQNIPIRSEEGRKIRKAFVAEKGWLLI 661
Query: 378 VADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMEL 437
AD + IE RVLA ++ ++ ++AF+ GED++ T +R F V VT + R I K +
Sbjct: 662 SADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVEIEDVTPNMRRIAKTINF 721
Query: 438 ALGY 441
+ Y
Sbjct: 722 GVVY 725
>gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 38.6 bits (90), Expect = 0.005
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 6/55 (10%)
Query: 68 IVAHNSYFERTVLKAC---FNLDIPIHRWICTLVLARS--NGLPSA-LKAVGEAL 116
++AHN+ F+ +VL+ +N+ +P +ICT+ LA++ + + +A L V L
Sbjct: 83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL 137
>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease
proofreading domain present in DNA polymerase I, Werner
syndrome helicase, RNase D and other enzymes.
Length = 172
Score = 37.3 bits (87), Expect = 0.012
Identities = 37/180 (20%), Positives = 63/180 (35%), Gaps = 38/180 (21%)
Query: 4 LFIDFETRSPIDLTKCGICKYAEDVCVILFAFG----FDDHPVELWDCVHDPVMPQVLKE 59
+ +D ET T Y+ + +I + F P+ L D + +LK+
Sbjct: 24 VALDTET------TGLNS--YSGKLVLIQISVTGEGAFIIDPLALGDDLE------ILKD 69
Query: 60 ALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLS 119
LE+ +T V HN+ F+ VL I + T++ A L L+
Sbjct: 70 LLEDETITKVGHNAKFDLHVLA---RFGIELENIFDTMLAAY------LLLGGPSKHGLA 120
Query: 120 SQ-KMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178
+ K G EL K + +P E +Y D ++++LE
Sbjct: 121 TLLKEYLGVELDKEEQKSDW------GARPLSEEQL----QYAAEDADALLRLYEKLEKE 170
>gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated.
Length = 557
Score = 37.2 bits (87), Expect = 0.014
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 51 PVMPQVLKEALE-NTDVTIVAHNSYFERTVLKA-CFNLDI--PIHRWICTLVLAR 101
P + +VL LE +VAHN+ F+ L+A P +CT+ LAR
Sbjct: 80 PPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLAR 134
>gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional.
Length = 219
Score = 33.9 bits (78), Expect = 0.14
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 18/78 (23%)
Query: 69 VAHNSYFERTVLKACFNLDIPIHRWICTLVLARS--NGLPSALKAVGEALKLSSQKMEEG 126
VAHN+ F+R VL ++P WICT+ LAR G+ + A+ ++ KL+ Q
Sbjct: 78 VAHNASFDRRVLP-----EMP-GEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPP-- 129
Query: 127 KELIARFCKGETHECLYD 144
L H LYD
Sbjct: 130 -GLHH-------HRALYD 139
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon;
Provisional.
Length = 313
Score = 32.4 bits (74), Expect = 0.37
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 9/57 (15%)
Query: 67 TIVAHNSYFERTVLKACFNL---DIPIHRWICTLVLARSNGLPSALKAVGEALKLSS 120
T+VAHN F+ + L A ++P+ + +CT+ LAR GL L+L +
Sbjct: 96 TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGL------PNLRLET 146
>gnl|CDD|151519 pfam11074, DUF2779, Domain of unknown function(DUF2779). This
domain is conserved in bacteria. The function is not
known.
Length = 127
Score = 31.8 bits (73), Expect = 0.60
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 57 LKEALENTDVTIVAHNSYFERTVLK 81
LK+A+ +IV +N FE+T LK
Sbjct: 61 LKKAIGKDYGSIVVYNKSFEKTRLK 85
>gnl|CDD|162272 TIGR01255, pyr_form_ly_1, formate acetyltransferase 1. This model
describes formate acetyltransferase 1. More distantly
related putative formate acetyltransferases have also
been identified, including formate acetyltransferase 2
from E. coli, which is excluded from this model.
Length = 744
Score = 31.0 bits (70), Expect = 1.1
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 474 EWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAW 510
W + N ++Q+N+ + ++ F+ ER K W
Sbjct: 9 NWRNKVNVRDFIQKNYKPYDGDESFLAGPTERTLKVW 45
>gnl|CDD|129770 TIGR00687, pyridox_kin, pyridoxal kinase. ThiD and related
proteins form an outgroup.
Length = 286
Score = 29.4 bits (66), Expect = 2.8
Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 18/69 (26%)
Query: 285 RSAVLKLNTL---VEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQ 341
R+A L L V A+N T+QF + G+W+G V PP L E +D
Sbjct: 19 RAATFPLQRLGFEVWAVN-------TVQFSNHTGYGKWTGQVLPPDEL------TELVDG 65
Query: 342 I--ITHLPT 348
+ I L
Sbjct: 66 LAAINKLNQ 74
>gnl|CDD|180238 PRK05756, PRK05756, pyridoxamine kinase; Validated.
Length = 286
Score = 29.1 bits (66), Expect = 3.5
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 10/49 (20%)
Query: 285 RSAVLKLNTL---VEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLP 330
+AV + L V +N T+QF + G+W+GCV PP +L
Sbjct: 19 SAAVFPMQRLGVNVWPLN-------TVQFSNHTGYGKWTGCVMPPSHLT 60
>gnl|CDD|173399 PTZ00107, PTZ00107, hexokinase; Provisional.
Length = 464
Score = 28.9 bits (65), Expect = 4.0
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 71 HNSYFERTVLKACFNLDIPIH-----RWICTLVLARSNGLPSALKA 111
+ F R V+K +++D+ R IC LV R+ L +A A
Sbjct: 348 PDLQFSRQVIKEAWDVDLTDEDLYTIRKICELVRGRAAQLAAAFIA 393
>gnl|CDD|128862 smart00595, MADF, subfamily of SANT domain.
Length = 89
Score = 28.9 bits (65), Expect = 5.0
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 137 ETHECLYDRNKPNHR------EAWRLFGEYCKGDVTVTREIFKRL 175
CL+DR P++R +AW E V ++ +K L
Sbjct: 7 RERPCLWDRRHPDYRNKEEKRKAWEEIAEELGLSVEECKKRWKNL 51
>gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit
beta; Validated.
Length = 356
Score = 28.4 bits (63), Expect = 5.6
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 6 IDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDH 40
I E RSP ++ CG C+ A DV V AF H
Sbjct: 294 IPIEERSPEEVLTCGGCRIAPDVDVYNPAFDVTPH 328
>gnl|CDD|151247 pfam10797, YhfT, Protein of unknown function. This family is
conserved in Firmicutes and Proteobacteria. The function
is not known but several members are annotated as being
homologues of E coli YhfT, a protein thought to be
involved in fatty acid oxidation.
Length = 421
Score = 28.4 bits (64), Expect = 6.4
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 430 AIGKVMELALGYQGGAKAFQKMASTTG 456
A+ +++E+AL GGA A KMA TG
Sbjct: 352 AMTRLLEVAL-LIGGANAANKMAPGTG 377
>gnl|CDD|184639 PRK14346, PRK14346, lipoate-protein ligase B; Provisional.
Length = 230
Score = 28.2 bits (63), Expect = 6.4
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 38 DDHPVELWDCVHDPVMPQVLKEALENT----DVTIVAHN 72
+ P ELW C H PV Q L ++ D+ +VA N
Sbjct: 29 PETPDELWICEHPPVYTQGLAGKADHVLNPGDIPVVATN 67
>gnl|CDD|182034 PRK09698, PRK09698, D-allose kinase; Provisional.
Length = 302
Score = 28.0 bits (63), Expect = 8.2
Identities = 5/17 (29%), Positives = 11/17 (64%)
Query: 483 RWMQENHPEHAIEDLFI 499
RW ++ ++ + DLF+
Sbjct: 193 RWYEQQPRDYPLSDLFV 209
>gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 27.9 bits (63), Expect = 8.2
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 55 QVLKEALENTDVTI-VAHNSYFERTVLKACF---NLDIPIHRWICTLVLAR 101
+VL + E +I VAHN+ F+ + + L+ + I TL L+R
Sbjct: 488 EVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSR 538
>gnl|CDD|182592 PRK10619, PRK10619, histidine/lysine/arginine/ornithine transporter
subunit; Provisional.
Length = 257
Score = 28.0 bits (62), Expect = 8.6
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 112 VGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNH 150
VGE L++ Q EEGK ++ THE + R+ +H
Sbjct: 188 VGEVLRIMQQLAEEGKTMVV-----VTHEMGFARHVSSH 221
>gnl|CDD|151090 pfam10545, MADF_DNA_bdg, Alcohol dehydrogenase transcription factor
Myb/SANT-like. The myb/SANT-like domain in Adf-1 (MADF)
is an approximately 80-amino-acid module that directs
sequence specific DNA binding to a site consisting of
multiple tri-nucleotide repeats. The MADF domain is
found in one or more copies in eukaryotic and viral
proteins and is often associated with the BESS domain.
It is likely that the MADF domain is more closely
related to the myb/SANT domain than it is to other HTH
domains.
Length = 84
Score = 28.1 bits (63), Expect = 8.7
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 129 LIARFCKGETHECLYDRNKPNHR------EAWRLFGEYCKGDVTVTREIFKR 174
LI K H CL+DR+ P++R AW E DV V E KR
Sbjct: 1 LIELVRK---HPCLWDRSHPDYRNKELRERAWEEIAEELGEDVDVE-ECKKR 48
>gnl|CDD|163533 TIGR03821, AblA_like_1, lysine-2,3-aminomutase-related protein.
Members of this protein form a distinctive clade,
homologous to lysine-2,3-aminomutase (of Bacillus,
Clostridium, and methanogenic archaea) and likely
similar in function. Members of this family are found in
E. coli, Buchnera, Yersinia, etc.
Length = 321
Score = 27.7 bits (62), Expect = 9.2
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 143 YDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTIND 194
Y N+PN + W+ EY + I +PL +K+ L +L +
Sbjct: 120 YQENQPNKAQ-WKEALEYIAQHPEINEVILSGGDPLMAKDHRLDWLLNLLEQ 170
>gnl|CDD|179363 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 27.7 bits (63), Expect = 9.7
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 12/48 (25%)
Query: 591 YTYGGK------LTENIVQAVSR---DILAEGMMNA--TKAGYDIVLT 627
YT+GG+ E + +IL M+ TK GYD+ LT
Sbjct: 143 YTHGGRKPTGLDAVEWAKEVEELGAGEILLT-SMDRDGTKNGYDLELT 189
>gnl|CDD|177948 PLN02314, PLN02314, pectinesterase.
Length = 586
Score = 27.9 bits (62), Expect = 9.8
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 57 LKEALENTDVTIVAHNSY-FERTVLKACFNLDIPIHRWICTLVLARSNGLPS 107
+K A+ N+ T NS +L +L IPIHR + + S+G PS
Sbjct: 212 VKTAMSNS--TEFTSNSLAIVSKILGILSDLGIPIHRRLLSFHHDLSSGFPS 261
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.133 0.403
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 10,920,933
Number of extensions: 701189
Number of successful extensions: 1391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1383
Number of HSP's successfully gapped: 35
Length of query: 675
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 575
Effective length of database: 3,833,673
Effective search space: 2204361975
Effective search space used: 2204361975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.9 bits)