RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781038|ref|YP_003065451.1| putative DNA-binding/iron
metalloprotein/AP endonuclease [Candidatus Liberibacter asiaticus str.
psy62]
(363 letters)
>gnl|CDD|30879 COG0533, QRI7, Metal-dependent proteases with possible chaperone
activity [Posttranslational modification, protein
turnover, chaperones].
Length = 342
Score = 403 bits (1036), Expect = e-113
Identities = 166/344 (48%), Positives = 218/344 (63%), Gaps = 13/344 (3%)
Query: 8 VIGIETSCDETAVAVVRRKDSHGEILAEAVLSQIDQHGHYGGVVPEVAARAHVDVLDILI 67
++GIETSCDET VA+V +ILA V SQI+ H YGGVVPE+A+R HV+ + LI
Sbjct: 3 ILGIETSCDETGVAIVD----EEKILANVVASQIELHARYGGVVPELASRHHVENIPPLI 58
Query: 68 KQTLLRANMQISDMDSIAVTAGPGLMGGLIVGLMTAKAISYVSHKPFYAINHLEGHILTA 127
++ L A + + D+D+IAVTAGPGL G L+VG AKA++ +KP +NHLEGHI A
Sbjct: 59 EEALAEAGVSLEDIDAIAVTAGPGLGGALLVGATAAKALALALNKPLIPVNHLEGHIEAA 118
Query: 128 RLTDDIAFPYLVLLVSGGHTQILLVRDVAHYDRLGTTIDDALGECFDKIAKSLGLPYPGG 187
RL +AFP + LLVSGGHTQ++ VR + Y+ LG T+DDA GE FDK+A+ LGL YPGG
Sbjct: 119 RLETGLAFPPVALLVSGGHTQLIAVRGIGRYEVLGETLDDAAGEAFDKVARLLGLGYPGG 178
Query: 188 VEIEKAALMGDGKRFKFPCPLVQGTLCDFSFSGLKTSVQKTICAF---DVLEKQDIADIC 244
IEK A GD F+FP P+V+G DFSFSGLKT+V + + + L ++D DI
Sbjct: 179 PAIEKLAKKGDPDAFEFPRPMVKGKNLDFSFSGLKTAVLRLLKKLKQKEELNEEDKEDIA 238
Query: 245 ASFQVTVVRILQARLKQGFLLFRKAFPHKQAVLVVSGGVASNHFIRASLIDLCVLHGFRF 304
ASFQ V +L + ++ K LV++GGVA+N +R L ++C G
Sbjct: 239 ASFQEAVFDMLVEKTERALKHTGKKE------LVIAGGVAANSRLREMLEEMCKERGAEV 292
Query: 305 VAPPARLCTDNAVMIAWAALERMEAGLPADDLSISPRSRWPLDE 348
PP LCTDNA MIA+A L R +AG L ++ R RW LDE
Sbjct: 293 YIPPLELCTDNAAMIAYAGLLRYKAGRFISPLDVNVRPRWRLDE 336
>gnl|CDD|37918 KOG2707, KOG2707, KOG2707, Predicted metalloprotease with chaperone
activity (RNAse H/HSP70 fold) [Posttranslational
modification, protein turnover, chaperones].
Length = 405
Score = 299 bits (766), Expect = 1e-81
Identities = 144/359 (40%), Positives = 194/359 (54%), Gaps = 18/359 (5%)
Query: 4 IKKTVIGIETSCDETAVAVVRRKDSHGEILAEAVLSQIDQHGHYGGVVPEVAARAHVDVL 63
+ V+GIETSCD+TAVAVV D +L+ + S+ + H YGG++P VA H + +
Sbjct: 30 LSYKVLGIETSCDDTAVAVV---DEFSHVLSSEIYSRTEIHRQYGGIIPTVAQLLHRENI 86
Query: 64 DILIKQTLLRANMQISDMDSIAVTAGPGLMGGLIVGLMTAKAISYVSHKPFYAINHLEGH 123
LI++ L A + D+D+IAVT GPGL L VGL AK ++ KP ++H+E H
Sbjct: 87 PRLIQRALDAAGLSPKDLDAIAVTRGPGLPLSLKVGLSFAKGLAVKLQKPLIPVHHMEAH 146
Query: 124 ILTARLTDD-IAFPYLVLLVSGGHTQILLVRDVAHYDRLGTTIDDALGECFDKIAKSLGL 182
L+ RL DD + FP+L LLVSGGHT ++L V ++ LG T+D A GE DK A+ LGL
Sbjct: 147 ALSIRLVDDSVRFPFLALLVSGGHTLLVLANGVGDHELLGQTVDIAPGEALDKCARRLGL 206
Query: 183 P------YPGGVEIEKAALMGD-GKRFKFPCPLVQGTLCDFSFSGLKTSVQKTICAFDVL 235
GG IE A KFP PL C+FSFSGLKTS ++ I +
Sbjct: 207 LGHPEDARSGGKAIEHLANRASADLHLKFPIPLKNVKKCNFSFSGLKTSYRRIIEKLEKN 266
Query: 236 EK--QDIADICASFQVTVVRILQARLKQGFLLFRKAFPHKQAVLVVSGGVASNHFIRASL 293
E+ +IAD AS Q TV R + ++ + + P LV+SGGVASN +IR +L
Sbjct: 267 EETLSEIADFAASLQRTVFRHISSKTHR-AIKSLLLQPKNVKQLVISGGVASNQYIRGAL 325
Query: 294 IDLCVLHGFRFVAPPARLCTDNAVMIAWAALERMEAGLPA----DDLSISPRSRWPLDE 348
L H + PP LC+DN +MIAW +E + G D I R L E
Sbjct: 326 EKLSAAHNCTSIKPPPSLCSDNGIMIAWTGIEMLRNGRELTSIPDIEPIRARPDNGLLE 384
>gnl|CDD|144420 pfam00814, Peptidase_M22, Glycoprotease family. The Peptidase M22
proteins are part of the HSP70-actin superfamily. The
region represented here is an insert into the fold and
is not found in the rest of the family (beyond the
Peptidase M22 family). Included in this family are the
Rhizobial NodU proteins and the HypF regulator. This
region also contains the histidine dyad believed to
coordinate the metal ion and hence provide catalytic
activity. Interestingly the histidines are not well
conserved, and there is a lack of experimental evidence
to support peptidase activity as a general property of
this family. There also appear to be instances of this
domain outside of the HSP70-actin superfamily.
Length = 225
Score = 212 bits (543), Expect = 8e-56
Identities = 108/292 (36%), Positives = 142/292 (48%), Gaps = 68/292 (23%)
Query: 31 EILAEAVLSQIDQHGHYGGVVPEVAARAHVDVLDILIKQTLLRANMQISDMDSIAVTAGP 90
EILA +LSQ D H YG VVPE+A+R H + L LI++ L A + + D+D+IAVTAGP
Sbjct: 1 EILANVILSQKDLHAPYG-VVPELASRHHSERLLPLIEEALAEAGLSLEDLDAIAVTAGP 59
Query: 91 GLMGGLIVGLMTAKAISYVSHKPFYAINHLEGHILTARLTDDIAFPYLVLLVSGGHTQIL 150
GL GL VG AK ++ KP +NHLE H L ARLT+ +VLLVSGGHTQ+
Sbjct: 60 GLFTGLRVGATFAKGLALALDKPLVGVNHLEAHALAARLTE----GPVVLLVSGGHTQVY 115
Query: 151 LVRDVAHYDRLGTTIDDALGECFDKIAKSLGLPYPGGVEIEKAALMGDGKRFKFPCPLVQ 210
+D Y+ LG T+DDA GE FDK+A++
Sbjct: 116 AAKDGR-YEILGETLDDAAGEAFDKVARA------------------------------- 143
Query: 211 GTLCDFSFSGLKTSVQKTICAFDVLEKQDIADICASFQVTVVRILQARLKQGFLLFRKAF 270
+ + + DI ASFQ V L + + +A
Sbjct: 144 -------------------VLRLLEKLKKKEDIAASFQEAVFDHLAEKTE-------RAL 177
Query: 271 PHKQA-VLVVSGGVASNHFIRASLIDLCVLHGFRFVAPPARLCTDNAVMIAW 321
H A LV+ GGVA+N +R +L ++ V APP CTDN MIAW
Sbjct: 178 KHTGAKELVILGGVAANKRLREALTEMAVER----FAPPLEYCTDNGAMIAW 225
>gnl|CDD|37919 KOG2708, KOG2708, KOG2708, Predicted metalloprotease with chaperone
activity (RNAse H/HSP70 fold) [Posttranslational
modification, protein turnover, chaperones].
Length = 336
Score = 149 bits (378), Expect = 9e-37
Identities = 109/343 (31%), Positives = 162/343 (47%), Gaps = 27/343 (7%)
Query: 8 VIGIETSCDETAVAVVRRKDSHGEILAEAVLSQIDQHGHYGGVVPEVAARAHVDVLDILI 67
+G+E S ++ V +VR G+ILA + I G G +P AR H + L+
Sbjct: 4 ALGLEGSANKLGVGIVR----DGKILANPRHTYITPPGE--GFLPRDTARHHRAWILGLV 57
Query: 68 KQTLLRANMQISDMDSIAVTAGPGLMGGLIVGLMTAKAISYVSHKPFYAINHLEGHILTA 127
KQ L A + D+D I T GPG+ L V + A+ +S + +KP +NH GHI
Sbjct: 58 KQALEEAGVTSDDIDCICYTKGPGMGAPLSVVAIVARTLSLLWNKPLVGVNHCIGHIEMG 117
Query: 128 RLTDDIAFPYLVLLVSGGHTQILLVRDVAHYDRLGTTIDDALGECFDKIAKSLGL---PY 184
R P +VL VSGG+TQ++ + Y G T+D A+G C D+ A+ L L P
Sbjct: 118 REITGAQNP-VVLYVSGGNTQVIAYSE-KRYRIFGETLDIAVGNCLDRFARVLKLSNDPS 175
Query: 185 PGGVEIEKAALMGDGKRF-KFPCPLVQGTLCDFSFSGLKTSVQKTIC-AFDVLEKQDIAD 242
P G IE+ A GK + + P V+G D SFSG+ + ++ + D
Sbjct: 176 P-GYNIEQLA--KKGKNYIELPY-TVKGM--DVSFSGILSYIEDLAEELLKPSSEVTKED 229
Query: 243 ICASFQVTVVRILQARLKQGFLLFRKAFPHKQAVLVVSGGVASNHFIRASLIDLCVLHGF 302
+C S Q TV +L ++ A + VL+V GGV N ++ + +C G
Sbjct: 230 LCYSLQETVFAMLVEITERAM-----AHCGSKEVLIV-GGVGCNERLQEMMAIMCSERGG 283
Query: 303 RFVAPPARLCTDNAVMIAWAALERMEAG--LPADDLSISPRSR 343
+ A R C DN VMIA A L +G P + +++ R R
Sbjct: 284 KLFATDERFCIDNGVMIAQAGLLMFRSGARTPLSESTVTQRYR 326
>gnl|CDD|31407 COG1214, COG1214, Inactive homolog of metal-dependent proteases,
putative molecular chaperone [Posttranslational
modification, protein turnover, chaperones].
Length = 220
Score = 53.5 bits (128), Expect = 9e-08
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 2/95 (2%)
Query: 27 DSHGEILAEAVLSQIDQHGHYGGVVPEVAARAHVDVLDILIKQTLLRANMQISDMDSIAV 86
D+ L+ A+ + G E R H + L +I + L A + + D+D+IAV
Sbjct: 7 DTSTSALSVALY--LADDGKVLAEHTEKLKRNHAERLMPMIDELLKEAGLSLQDLDAIAV 64
Query: 87 TAGPGLMGGLIVGLMTAKAISYVSHKPFYAINHLE 121
GPG GL +G+ AK ++ + P ++ LE
Sbjct: 65 AKGPGSFTGLRIGVAFAKGLALALNIPLVGVSSLE 99
>gnl|CDD|30417 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 38.0 bits (88), Expect = 0.004
Identities = 33/155 (21%), Positives = 51/155 (32%), Gaps = 20/155 (12%)
Query: 169 LGECFDKIAKSLGL----PYPG--GVEIEKAALMGDGKRFKFPCPLVQGTLCDFSFSGLK 222
+G FD +A LG+ Y G + +E A DG + + + D LK
Sbjct: 597 IGRVFDAVAALLGICETRTYEGEAAMALEALADQSDGVDYPYEIKNEDNQVLD-----LK 651
Query: 223 TSVQKTICAFDVLEKQDIADICASFQVTVVRILQARLKQGFLLFRKAFPHKQAVLVVSGG 282
+ + E + IA F + + K + + VL SGG
Sbjct: 652 ELILGVLEDLLKDEPEKIA---TKFHNALAEGFAELAVE----LAKKYGINKVVL--SGG 702
Query: 283 VASNHFIRASLIDLCVLHGFRFVAPPARLCTDNAV 317
V N + L GFRF+ D +
Sbjct: 703 VFQNRLLLERLAKYLKKEGFRFLFHQEVPAGDGGI 737
>gnl|CDD|35084 COG5525, COG5525, Bacteriophage tail assembly protein [General
function prediction only].
Length = 611
Score = 29.9 bits (67), Expect = 1.1
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 185 PGGVEIEKAALMGDGKRFKFPCP 207
PG IE+A GD +RF PCP
Sbjct: 209 PGTTTIERAYNAGDQRRFYVPCP 231
>gnl|CDD|30788 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 29.8 bits (67), Expect = 1.3
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 21/87 (24%)
Query: 291 ASLIDLCVLHGFRFVAPPA---RLCTDNAVMIAWAALERMEAGLP------------ADD 335
A+ + C G F+ P A R D A +AG+P +
Sbjct: 89 AAFAEACAEAGLTFIGPSAEAIRRMGDKITARRLMA----KAGVPVVPGSDGAVADNEEA 144
Query: 336 LSISPRSRWPLDEKAPSKIGSGKRGVK 362
L+I+ +P+ KA + G G RG++
Sbjct: 145 LAIAEEIGYPVIVKAAA--GGGGRGMR 169
>gnl|CDD|111443 pfam02543, CmcH_NodU, Carbamoyltransferase. This family consists
of NodU from Rhizobium and CmcH from Nocardia
lactamdurans. NodU a Rhizobium nodulation protein
involved in the synthesis of nodulation factors has
6-O-carbamoyltransferase-like activity. CmcH is involved
in cephamycin (antibiotic) biosynthesis and has
3-hydroxymethylcephem carbamoyltransferase activity,
EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate
+ 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate +
3-carbamoyloxymethylcephem.
Length = 360
Score = 28.9 bits (65), Expect = 2.0
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 216 FSFSGLKTSVQKTICAFDVLEKQDIADICASFQVTVVRILQARLKQGFLLFRKAFPHKQA 275
S LKT +L++++ DI AS Q T+ R+++ L+ + F
Sbjct: 112 LGPSLLKTHDVFRKSMLSLLKQREE-DIAASAQRTLERLVEELLRHVYEEF-----GIDR 165
Query: 276 VLVVSGGVASN 286
L ++GGVA N
Sbjct: 166 NLCIAGGVALN 176
>gnl|CDD|88574 cd05134, RasGAP_RASA3, RASA3 (or GAP1_IP4BP) is a member of the
GAP1 family and has been shown to specifically bind
1,3,4,5-tetrakisphosphate (IP4). Thus, RASA3 may
function as an IP4 receptor. The members of GAP1 family
are characterized by a conserved domain structure
comprising N-terminal tandem C2 domains, a highly
conserved central RasGAP domain, and a C-terminal
pleckstrin-homology domain that is associated with a
Bruton's tyrosine kinase motif. Purified RASA3
stimulates GAP activity on Ras with about a five-fold
lower potency than p120RasGAP, but shows no
GAP-stimulating activity at all against Rac or Rab3A..
Length = 310
Score = 28.9 bits (64), Expect = 2.2
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 10/66 (15%)
Query: 35 EAVLSQIDQHGHYGGVVPEVAARAHVDVLDILIKQTLLRAN----------MQISDMDSI 84
EA + + HYG +VP ++A A +V T+ R N M+++ M +
Sbjct: 36 EAAIPLVRLFLHYGKIVPFISAIASAEVNRTQDPNTIFRGNSLTSKCIDETMKLAGMHYL 95
Query: 85 AVTAGP 90
VT P
Sbjct: 96 QVTLKP 101
>gnl|CDD|31008 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 28.7 bits (63), Expect = 2.7
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 235 LEKQDIADICASFQVTVVRILQARLKQGFLLFRKA 269
L +D+A+ + TV RIL+ K G + R
Sbjct: 172 LTHKDLAEYLGLSRETVSRILKELRKDGLISVRGK 206
>gnl|CDD|145708 pfam02698, DUF218, DUF218 domain. This large family of proteins
contains several highly conserved charged amino acids,
suggesting this may be an enzymatic domain (Bateman A
pers. obs). The family includes SanA, which is involved
in Vancomycin resistance. This protein may be involved
in murein synthesis.
Length = 148
Score = 28.4 bits (64), Expect = 3.2
Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 30/92 (32%)
Query: 252 VRILQARLKQGFLLFRKAFPHKQAVLVVSGGVASNHFIRASLIDLCVLHGFRFVAPPARL 311
L ARL L+R ++VSGG A
Sbjct: 12 SPALAARLDAAAELYRA---GPAPRIIVSGG-----------------------AGGGEP 45
Query: 312 CTDNAVMIAWAALERMEAGLPADDLSISPRSR 343
++ VM + +E G+PA+ + + P+SR
Sbjct: 46 VSEAEVMRRYL----VELGVPAEAILLEPQSR 73
>gnl|CDD|39796 KOG4596, KOG4596, KOG4596, Uncharacterized conserved protein
[Function unknown].
Length = 1936
Score = 28.1 bits (62), Expect = 3.5
Identities = 31/165 (18%), Positives = 53/165 (32%), Gaps = 12/165 (7%)
Query: 168 ALGECFDKIAKSLGLPYPGGVEIEK-----AALMGDGKRFKFPCPLVQGTLCDFSF--SG 220
ALG + G P G+ ++ +AL KR L +L
Sbjct: 24 ALGHKLPTTSGGTGGPSTSGLGSKRKRDARSALCSPPKRTL--GNLANASLQSSHLVSPN 81
Query: 221 LKTSVQKTI-CAFDVLEKQDIADICASFQVTVVRILQARLKQGFLLFRKAFPHKQAVLVV 279
L TI + +K A I A + ++ LKQ F+ K + +L
Sbjct: 82 LDQWKDFTINLNIETFQKSIQAAILAGHFTKIAKMFCGALKQFFVGRAKKDKVELLILGY 141
Query: 280 SGGVASNHFIRASLIDLCVLHGFRFVAPPARLCTDNAVMIAWAAL 324
N F +L + L ++ +N + + + L
Sbjct: 142 IAKTVPNIF--DTLNVIPALRSLLRRIANSKSYPNNILELLISNL 184
>gnl|CDD|34211 COG4573, GatZ, Predicted tagatose 6-phosphate kinase
[Carbohydrate transport and metabolism].
Length = 426
Score = 28.0 bits (62), Expect = 4.7
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 9 IGIETSCD------ETAVAVVRRKDSHGEILAEAVLSQIDQHGHYGGVVPE 53
IGI + C E A+ R + +L EA +Q++Q G Y G+ P
Sbjct: 17 IGIYSVCSAHPLVIEAALRFARASQT--PVLIEATSNQVNQFGGYTGMTPA 65
>gnl|CDD|30988 COG0643, CheA, Chemotaxis protein histidine kinase and related
kinases [Cell motility and secretion / Signal
transduction mechanisms].
Length = 716
Score = 27.6 bits (61), Expect = 6.0
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 145 GHTQILLVRDVAHYDRLGTTIDDALGECFDKIAKSLGLPYPGGVEIEKAALMGDGK 200
+++VR R+ +D+ +G+ + + K LG I A ++GDG
Sbjct: 643 EQGPVVIVRSGGG--RVALLVDELIGQ-QEVVIKPLGGNLAKVPGISGATILGDGS 695
>gnl|CDD|143487 cd06812, PLPDE_III_DSD_D-TA_like_1, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes Similar to D-Serine Dehydratase
and D-Threonine Aldolase, Unknown Group 1. This
subfamily is composed of uncharacterized bacterial
proteins with similarity to eukaryotic D-serine
dehydratases (DSD) and D-threonine aldolases (D-TA). DSD
catalyzes the dehydration of D-serine to aminoacrylate,
which is rapidly hydrolyzed to pyruvate and ammonia.
D-TA reversibly catalyzes the aldol cleavage of
D-threonine into glycine and acetaldehyde, and the
synthesis of D-threonine from glycine and acetaldehyde.
DSD and D-TA are fold type III PLP-dependent enzymes,
similar to bacterial alanine racemase (AR), which
contains an N-terminal PLP-binding TIM barrel domain and
a C-terminal beta-sandwich domain. AR exists as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. Based on
their similarity to AR, it is possible members of this
family also form dimers in solution.
Length = 374
Score = 27.3 bits (61), Expect = 6.3
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 17 ETAVAVVRRKDSHGEILAEAVLSQIDQHGHYGGVVPE 53
E A AV HG VL +ID GH GG+ P+
Sbjct: 109 EQAQAVAAFSRQHGVRFP--VLIEIDCDGHRGGIAPD 143
>gnl|CDD|37574 KOG2363, KOG2363, KOG2363, Protein subunit of nuclear ribonuclease
P (RNase P) [Translation, ribosomal structure and
biogenesis].
Length = 247
Score = 26.8 bits (59), Expect = 9.8
Identities = 9/47 (19%), Positives = 15/47 (31%)
Query: 316 AVMIAWAALERMEAGLPADDLSISPRSRWPLDEKAPSKIGSGKRGVK 362
L L D ++ + R P K + + KRG+
Sbjct: 91 VRPKNIEGLSGACTMLDPDVITFNYTERLPFLFKRKEIMTAVKRGIF 137
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
0.324 0.139 0.411
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,309,206
Number of extensions: 231488
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 492
Number of HSP's successfully gapped: 26
Length of query: 363
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 268
Effective length of database: 4,210,882
Effective search space: 1128516376
Effective search space used: 1128516376
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: 41 (22.0 bits)
S2: 58 (25.9 bits)