RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780804|ref|YP_003065217.1| DNA polymerase III subunit
delta [Candidatus Liberibacter asiaticus str. psy62]
(352 letters)
>gnl|CDD|180631 PRK06585, holA, DNA polymerase III subunit delta; Reviewed.
Length = 343
Score = 168 bits (427), Expect = 3e-42
Identities = 86/331 (25%), Positives = 161/331 (48%), Gaps = 10/331 (3%)
Query: 18 FLSHF-----VFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWN 72
FL+ + YG D+GL+ E + K++ DPF++V L+ ++ + + +
Sbjct: 12 FLARPDPKIRAVLLYGPDRGLVRERARRLAKSVVPDLDDPFAVVRLDGDDLDADPARLED 71
Query: 73 EINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAE 132
E N+ SLF +++I + + K + L+ ++ + I+I++ ++KK ++LRK+ E
Sbjct: 72 EANAISLFGGRRLIWVR--AGSKNLAAALKALLESPPGDAFIVIEAGDLKKGSSLRKLFE 129
Query: 133 KFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLS 192
AI CY D++ L LI++ L I+ +A+ +L+A LGGDR+ASRNE++KL+
Sbjct: 130 TAAYAAAIPCYADDERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLA 189
Query: 193 SYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLH 252
Y IT V+ ++ D L +++ +A + G + D LA +L
Sbjct: 190 LYAHGKGEITLDDVRAVVGDASALSLDDAADAALAGDLAAFERALDRALAEGTAPVLILR 249
Query: 253 GFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKR-NILQESLRIWNKNLVRETLH 311
L+ FQ L + + E + + I + + + KR +++LR W+ + L
Sbjct: 250 AALRHFQRLHIVRLKVENGKSAEQAI--ASLRPPVFFKRKPDFEKALRRWSLERLLRALE 307
Query: 312 KIDHRIHLARKKKYLEKNIIFQTILYIAQTA 342
++ R+ L I + +L IA A
Sbjct: 308 RLQAAELDCRRNPALADAIARRVLLSIAVRA 338
>gnl|CDD|162213 TIGR01128, holA, DNA polymerase III, delta subunit. subunit around
DNA forming a DNA sliding clamp.
Length = 302
Score = 70.0 bits (172), Expect = 9e-13
Identities = 46/229 (20%), Positives = 101/229 (44%), Gaps = 21/229 (9%)
Query: 57 VLNALEIQKNISTF------WNEI----NSTSLFSKKKIILIENLSTEKKVLDCLEEIII 106
L + N+ WN++ + LFS+++++ + N E K + +
Sbjct: 11 ALAQGFDEFNVFRIDGEEFDWNQLLEEAQTLPLFSERRLVELRNP--EGKPGAKGLKALE 68
Query: 107 KNICN----HIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQ 162
+ + N +++I++ ++ K L K + + + C + L I+ L
Sbjct: 69 EYLANPPPDTLLLIEAPKLDKRKKLTKWLKALKNAQIVECKTPKEQELPRWIQARLKKLG 128
Query: 163 KSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEII 222
I +A Q+L + G+ +A EL+KL+ Y D IT + V++ + D+ + ++
Sbjct: 129 LRIDPDAVQLLAELVEGNLLAIAQELEKLALY-APDGKITLEDVEEAVSDSARFNVFDLT 187
Query: 223 NATIQGKIYNAI-MLADFFLASKMPSHALLHGFLQK-FQLLEKIHIIKE 269
+A ++GK A+ +L + P +L LQ+ +LL ++ + +
Sbjct: 188 DALLEGKAARALRILKGLLGEGEEP--LILLALLQRQLRLLLQLKRLAQ 234
>gnl|CDD|180139 PRK05574, holA, DNA polymerase III subunit delta; Reviewed.
Length = 340
Score = 51.7 bits (125), Expect = 2e-07
Identities = 48/227 (21%), Positives = 98/227 (43%), Gaps = 17/227 (7%)
Query: 23 VFIFYGSDKGLIFELINQF-KKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFS 81
+++ YG + L+ E + + + + ++ + E + S LFS
Sbjct: 19 LYLLYGDEPLLLQEAKDAIRAAARAQGFDE-RNVFTFDGSET--DWDDVLEACQSLPLFS 75
Query: 82 KKKIILI---ENLSTEK--KVLDCLEEIIIKNICNHIIII----KSNEIKKNNTLRKIAE 132
+K++ + E L+ K K L LE + +++I K ++ KK + K +
Sbjct: 76 DRKLVELRLPEFLTGAKGEKALKRLEAYLNPLPHPDLLLIVRLPKLDKAKKKSAWFKALK 135
Query: 133 KFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLS 192
K V + P + L I++ L I A Q+L + G+ +A EL+KL+
Sbjct: 136 KKAVV--VEAQPPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLA 193
Query: 193 SYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAI-MLAD 238
+ IT + V++ + D+ + ++++A + GKI A+ +L
Sbjct: 194 LLYPDGK-ITLEDVEEAVPDSARFDVFDLVDAILAGKIKRALRILDG 239
>gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 37.5 bits (88), Expect = 0.005
Identities = 47/240 (19%), Positives = 90/240 (37%), Gaps = 31/240 (12%)
Query: 3 TIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDP------FSLV 56
+ E K + + F F L E FK+ + ++ FS+
Sbjct: 27 SAEIEKVVVDKKSKKW--EFHLKF---PNILPIEDFKLFKEKLKQSFSHIADIKVTFSIE 81
Query: 57 VLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIII 116
V N ++ + +WNEI +KK L ++L ++KV +E N +II
Sbjct: 82 VENITFTEELLLDYWNEI---IEKAKKNSPLFKSLLKKQKVE--VEG-------NKLIIK 129
Query: 117 KSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHL-----MDLIEESLLIGQKSISKEAKQ 171
+NEI++++ +K K + KI + +E+ ++ K AK+
Sbjct: 130 VNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKLAKE 189
Query: 172 ILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIY 231
L A A + + K + I ++ K+ I + EE ++G ++
Sbjct: 190 ALEAM--KKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEITPMKEI-NEEERRVVVEGYVF 246
>gnl|CDD|148006 pfam06144, DNA_pol3_delta, DNA polymerase III, delta subunit. DNA
polymerase III, delta subunit (EC 2.7.7.7) is required
for, along with delta' subunit, the assembly of the
processivity factor beta(2) onto primed DNA in the DNA
polymerase III holoenzyme-catalysed reaction. The delta
subunit is also known as HolA.
Length = 172
Score = 35.7 bits (83), Expect = 0.016
Identities = 37/175 (21%), Positives = 73/175 (41%), Gaps = 10/175 (5%)
Query: 25 IFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKK 84
+ YG D L+ E +Q K + F+ + + E E + FS K+
Sbjct: 2 LLYGEDPFLLEETKDQILKAALDQGFEDFNYIYFDLEE--DWADDVLEECETLPFFSDKR 59
Query: 85 IILIENLSTEKKVLDC-----LEEII-IKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVL 138
I+++ N + ++ L+ LEE + +II ++ + L K+ +K
Sbjct: 60 IVILNNPNLKESKLNEKLLKRLEEYLSNPPEDTLLIIEAPGKLDERKKLTKLLKK--KAT 117
Query: 139 AISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSS 193
+ C+ + L+ I++ I K+A Q+L + + +A EL+KL+
Sbjct: 118 VVECFTLKEEELIQWIQKRAKELGLKIEKDALQLLAEKVENNLLAIAQELEKLAL 172
>gnl|CDD|181447 PRK08487, PRK08487, DNA polymerase III subunit delta; Validated.
Length = 328
Score = 31.8 bits (73), Expect = 0.28
Identities = 51/267 (19%), Positives = 103/267 (38%), Gaps = 11/267 (4%)
Query: 77 TSLFSKKKIILIE-NLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFT 135
+SLF K +++I+ + KK L L E+ KN N+ II K + K+ +K
Sbjct: 66 SSLFGGKNLLIIKLDKKIPKKELKLLIELCEKNSDNYFIIELYGADSKTKDIEKLFQKKD 125
Query: 136 SVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYC 195
+ + + N ++L++E I + A L D + NEL+KL+
Sbjct: 126 EAVFVRFFKPNAREALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAIL- 184
Query: 196 LEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFL 255
+ IT + +++++ + E+ + K + L ALL+
Sbjct: 185 --NEPITLKDIQELVFGLGSVSFEDFFEKLLNKKDIKDD--LEKLLEEGFNEIALLNSLE 240
Query: 256 QKFQLLEKIHI-IKECSNISFEKII-QKTEKNIIPMKRNILQESLRIWNKNLVRETLHKI 313
+ F L IK ++I+ K K I +++++I +
Sbjct: 241 RFFYQLFLFFAYIKINGKPDAKEILGYKPPKQIAENLA---KQAIKIKEAQYKEIFELLL 297
Query: 314 DHRIHLARKKKYLEKNIIFQTILYIAQ 340
+ + L +K + + T++ I +
Sbjct: 298 EWELELKTGQKIDKNLFLLSTLIKIQK 324
>gnl|CDD|128754 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 29.5 bits (67), Expect = 1.5
Identities = 26/115 (22%), Positives = 44/115 (38%), Gaps = 6/115 (5%)
Query: 124 NNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSIS-KEAKQILLANLGGDRI 182
N ++ EKF + ++ + + L +LI +K+ E +IL+ GG+
Sbjct: 11 NKATERLFEKFPTPEDLAAADEEE--LEELIRPLGFYRRKAKYLIELARILVEEYGGEVP 68
Query: 183 ASRNELQKLS---SYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAI 234
R EL KL +L I DTHVL I + + + +
Sbjct: 69 DDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEV 123
>gnl|CDD|185647 PTZ00468, PTZ00468, phosphofructokinase family protein; Provisional.
Length = 1328
Score = 28.8 bits (64), Expect = 2.3
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 78 SLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSV 137
+FS LIENL +K+ D EII+ + + + ++ K N + + FT
Sbjct: 1015 LIFSDIDERLIENLINSRKICDVRTEIILSALVQKELKFRRSKNKIKNGMNPVCFSFTDQ 1074
Query: 138 LAISCYP 144
+ +C P
Sbjct: 1075 VR-ACIP 1080
>gnl|CDD|178674 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 27.8 bits (62), Expect = 4.2
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 79 LFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEK 133
L+ K+K +L+ENL E K LD + I + I++ N K+ L ++ EK
Sbjct: 991 LYVKRKEVLLENLEYELKKLDN-KARFILAVVKGEIVV--NNRKRAELLAELEEK 1042
>gnl|CDD|185606 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 27.6 bits (61), Expect = 5.3
Identities = 25/109 (22%), Positives = 49/109 (44%), Gaps = 15/109 (13%)
Query: 111 NHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHL-----MDLIEESLLIGQKSI 165
N III ++ K+ + +R+ +KFT + H +D +ES+ I KS
Sbjct: 409 NSIIIGENYTSKRTSIIRQFTKKFT-------FFKKGEHNDGFSSVDSFKESVFIYPKSF 461
Query: 166 SKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTH 214
++ LL GG + +S N L++ + + T + ++ + T+
Sbjct: 462 K---EKELLTEKGGAQFSSANSLERGADEDYLIVNGTNEPYEEEVIKTN 507
>gnl|CDD|180982 PRK07452, PRK07452, DNA polymerase III subunit delta; Validated.
Length = 326
Score = 27.6 bits (62), Expect = 5.3
Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 150 LMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCL-EDILITEQHVKD 208
L L+E + ++ EA ++L +G D NEL+KL+ Y I+ + VK
Sbjct: 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKA 194
Query: 209 IICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMP 246
++ ++ +A +QG A+ L D L + P
Sbjct: 195 LV-SNTTQNSLQLADALLQGNTGKALALLDDLLDANEP 231
>gnl|CDD|165167 PHA02817, PHA02817, EEV Host range protein; Provisional.
Length = 225
Score = 26.8 bits (59), Expect = 8.3
Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 45 ISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEI 104
I + ++ + +N + I N F+N+IN+++ + KI+ I N++ + L +
Sbjct: 144 ICSRDNITYNKIYINKVNIDDN---FFNQINNSNTYYFDKILQINNVN--RYTLIFFVVV 198
Query: 105 IIKNICNHIIIIKSNEIKKNNTLR 128
IK + + I S K ++++
Sbjct: 199 SIKILFGFVFIFFSCNKKPLDSIK 222
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
0.323 0.137 0.386
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,495,647
Number of extensions: 357829
Number of successful extensions: 720
Number of sequences better than 10.0: 1
Number of HSP's gapped: 710
Number of HSP's successfully gapped: 55
Length of query: 352
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 258
Effective length of database: 3,963,321
Effective search space: 1022536818
Effective search space used: 1022536818
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.3 bits)