RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780741|ref|YP_003065154.1| carboxynorspermidine
decarboxylase [Candidatus Liberibacter asiaticus str. psy62]
(367 letters)
>gnl|CDD|143502 cd06829, PLPDE_III_CANSDC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Carboxynorspermidine
Decarboxylase. Carboxynorspermidine decarboxylase
(CANSDC) catalyzes the decarboxylation of
carboxynorspermidine, the last step in the biosynthesis
of norspermidine. It is homologous to eukaryotic
ornithine decarboxylase (ODC) and diaminopimelate
decarboxylase (DapDC), which are fold type III
PLP-dependent enzymes that contain an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain, similar to bacterial alanine
racemases. Based on this similarity, CANSDC may require
homodimer formation and the presence of the PLP cofactor
for its catalytic activity.
Length = 346
Score = 481 bits (1241), Expect = e-136
Identities = 153/347 (44%), Positives = 222/347 (63%), Gaps = 5/347 (1%)
Query: 4 TPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYEV 63
TP Y++D+ KL NL+ +++ +G K+LLALK F+ W +F + +Y+DGTT+SSL+E
Sbjct: 1 TPCYVLDEAKLRRNLEILKRVQERSGAKILLALKAFSMWSVFPLIREYLDGTTASSLFEA 60
Query: 64 MLGHEKFGGETHAYNVAYKDCEIDAVLSNCDTIIFNTVSQLNKFKDKAQKLHKKIGLRIN 123
LG E+FGGE H Y+ AY+D EID +L D IIFN++SQL +FKD+A+ +GLRIN
Sbjct: 61 RLGREEFGGEVHTYSPAYRDDEIDEILRLADHIIFNSLSQLERFKDRAKAAGISVGLRIN 120
Query: 124 PSVSYSKFILADPNRPFSRLGEKCKDKIESEIKNVNGLMFHNNCENKSFLCFSAMLKNIE 183
P S + L DP P SRLG + E ++ + GL FH CE F L+ +E
Sbjct: 121 PEYSEVETDLYDPCAPGSRLGVTLDELEEEDLDGIEGLHFHTLCEQ-DFDALERTLEAVE 179
Query: 184 KEFGHFITQIEWISLGGGIHFTDKDYPVKDFCQRLKEFSEKYSVQIYLEPGEAIVTNTTT 243
+ FG ++ Q++W++LGGG H T DY V +K F EKY V++YLEPGEA+ NT
Sbjct: 180 ERFGEYLPQLKWLNLGGGHHITRPDYDVDRLIALIKRFKEKYGVEVYLEPGEAVALNTGY 239
Query: 244 LNTTVLDISENIKNLVIVDSSVEAHVPDYLL--YQESATI--YPNTGPYTAMVCGRSCLA 299
L TVLDI EN + I+D+S AH+PD L Y+ P G +T + G SCLA
Sbjct: 240 LVATVLDIVENGMPIAILDASATAHMPDVLEMPYRPPIRGAGEPGEGAHTYRLGGNSCLA 299
Query: 300 GDIFGEFHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTIAVKN 346
GD+ G++ F++P+++GDR+ FED+A Y + + N FNG+ +P+IA+++
Sbjct: 300 GDVIGDYSFDEPLQVGDRLVFEDMAHYTMVKTNTFNGVRLPSIAIRD 346
>gnl|CDD|30369 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 256 bits (655), Expect = 8e-69
Identities = 93/370 (25%), Positives = 143/370 (38%), Gaps = 28/370 (7%)
Query: 2 IKTPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLY 61
TP Y+ D+ L N +G K+ A+K + + L + G +SL
Sbjct: 25 FGTPVYVYDEATLRRNARELKSAFPGSGAKVFYAVKANSNPAILRLLAEEGSGFDVASLG 84
Query: 62 EVMLGHEKF--GGETHAYNVAYKDCEIDAVLSNCD-TIIFNTVSQLNKFKDKAQKLHKKI 118
E+ L A + EI L I ++ +L + A L ++
Sbjct: 85 ELELALAAGFPPERIVFSGPAKSEEEIAFALELGIKLINVDSEEELERLSAIAPGLVARV 144
Query: 119 GLRINPSVSYSKFILADPNRPFSRLG-------EKCKDKIESEIKNVNGLMFHNNCENKS 171
LRINP VS S+ G + + + + GL FH +
Sbjct: 145 SLRINPGVSAGTHEYIATGGKSSKFGISPEEALDVLERAAKLLGLELVGLHFHIGSQITD 204
Query: 172 FLCFSAMLKNIEKEFGHFIT----QIEWISLGGGIHFT-DKDYPVKDFCQRLKEFSEKYS 226
F L +E+ FG Q+EW++LGGG+ T + +Y D K E +
Sbjct: 205 LDPFEEALAKVEELFGRLAEELGIQLEWLNLGGGLGITYEDEYDPPDLAAYAKALKEAFG 264
Query: 227 -----VQIYLEPGEAIVTNTTTLNTTVLDISEN-IKNLVIVDSSVEAHVPDYLLYQESAT 280
V++ LEPG AIV N L T VLD+ EN +N VIVD + + LY
Sbjct: 265 EYAEDVELILEPGRAIVANAGVLVTEVLDVKENGERNFVIVDGGMNDLMRP-ALYGAYHH 323
Query: 281 IYPN-----TGPYTAMVCGRSCLAGDIFG-EFHFEKPVKIGDRISFEDVAGYNINRKNWF 334
I N V G +C +GD+ + +P+K+GD + D Y + + +
Sbjct: 324 IRLNRTDEDAEREEYDVVGPTCESGDVLARDRALPEPLKVGDLLVILDAGAYGASMSSNY 383
Query: 335 NGINMPTIAV 344
NG P +
Sbjct: 384 NGRPRPAEVL 393
>gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Ornithine and Diaminopimelate
Decarboxylases, and Related Enzymes. This family
includes eukaryotic ornithine decarboxylase (ODC, EC
4.1.1.17), diaminopimelate decarboxylase (DapDC, EC
4.1.1.20), plant and prokaryotic biosynthetic arginine
decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine
decarboxylase (CANSDC), and ODC-like enzymes from
diverse bacterial species. These proteins are fold type
III PLP-dependent enzymes that catalyze essential steps
in the biosynthesis of polyamine and lysine. ODC and
ADC participate in alternative pathways of the
biosynthesis of putrescine, which is the precursor of
aliphatic polyamines in many organisms. ODC catalyzes
the direct synthesis of putrescine from L-ornithine,
while ADC converts L-arginine to agmatine, which is
hydrolysed to putrescine by agmatinase in a pathway that
exists only in plants and bacteria. DapDC converts
meso-2,6-diaminoheptanedioate to L-lysine, which is the
final step of lysine biosynthesis. CANSDC catalyzes the
decarboxylation of carboxynorspermidine, which is the
last step in the synthesis of norspermidine. The
PLP-dependent decarboxylases in this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist 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. Prokaryotic ornithine, lysine and
biodegradative arginine decarboxylases are fold type I
PLP-dependent enzymes and are not included in this
family.
Length = 368
Score = 147 bits (373), Expect = 5e-36
Identities = 83/369 (22%), Positives = 143/369 (38%), Gaps = 30/369 (8%)
Query: 4 TPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYEV 63
TP+Y+ D + + AL +GVKL A+K + TL + G +S E+
Sbjct: 1 TPFYVYDLDIIRAHYA-ALKEALPSGVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGEL 59
Query: 64 MLG-HEKFGGETHAYNVAYKDCE--IDAVLSNCDTIIFNTVSQLNKFKDKAQKLHK--KI 118
L E + K A+ S D I+ +++ +L + + A+KL +I
Sbjct: 60 ALALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARI 119
Query: 119 GLRINPSVSYSKFILADPNRPFSRLG------EKCKDKIESEIKNVNGLMFHNNCENKSF 172
LR+NP VS + S+ G ++ + + GL FH +
Sbjct: 120 LLRVNPDVS-AGTHKISTGGLKSKFGLSLSEARAALERAKELDLRLVGLHFHVGSQILDL 178
Query: 173 LCFSAMLKN---IEKEFGHFITQIEWISLGGG--IHFTDKDYPVKDFCQRLKEFSEKYS- 226
L + + +E +E + LGGG I + ++ +++ + +KY
Sbjct: 179 ETIVQALSDARELIEELVEMGFPLEMLDLGGGLGIPYDEQPLDFEEYAALINPLLKKYFP 238
Query: 227 ----VQIYLEPGEAIVTNTTTLNTTVLDISEN-IKNLVIVDSSVEAHVPDYLLYQESATI 281
V + LEPG IV L T V+ + N + +VD + L Y I
Sbjct: 239 NDPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGRFFAVVDGGMNHSFRPALAYDAYHPI 298
Query: 282 YP------NTGPYTAMVCGRSCLAGDIFGEFHFEKPVKIGDRISFEDVAGYNINRKNWFN 335
P + A + G C +GD+ G +++GD + FED+ Y + + FN
Sbjct: 299 TPLKAPGPDEPLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSESSNFN 358
Query: 336 GINMPTIAV 344
P +
Sbjct: 359 SHPRPAEYL 367
>gnl|CDD|143501 cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Diaminopimelate Decarboxylase.
Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20)
participates in the last step of lysine biosynthesis. It
converts meso-2,6-diaminoheptanedioate to L-lysine. It
is a fold type III PLP-dependent enzyme that contains an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. DapDC 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. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity.
Length = 373
Score = 75.6 bits (187), Expect = 2e-14
Identities = 80/370 (21%), Positives = 141/370 (38%), Gaps = 63/370 (17%)
Query: 4 TPYYLIDKQKLLNN---LDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSL 60
TP Y+ D+ + N L A G K+ A+K + + L + G S
Sbjct: 3 TPLYVYDEATIRENYRRLKEAF---SGPGFKICYAVKANSNLAILKLLAEEGLGADVVSG 59
Query: 61 YEVMLGHE-KFGGET---HAYNVAYKDCEIDAVLSNCDTIIFN--TVSQLNKFKDKAQKL 114
E+ + F E + + E++ L + N ++S+L + + A +L
Sbjct: 60 GELYRALKAGFPPERIVFTGNGKSDE--ELELALEL-GILRINVDSLSELERLGEIAPEL 116
Query: 115 HKK--IGLRINPSV------------SYSKF-ILADPNRPFSRLGEKCKDKIESEIKNVN 159
K + LR+NP V SKF I P + E + E +
Sbjct: 117 GKGAPVALRVNPGVDAGTHPYISTGGKDSKFGI------PLEQALEAYRRAKELPGLKLV 170
Query: 160 GLMFH---NNCENKSFLCFSAMLKNIEKEFGHFITQIEWISLGGG--IHFTDKDYP--VK 212
GL H + + F+ + L ++ E +E++ LGGG I + D+D P ++
Sbjct: 171 GLHCHIGSQILDLEPFVEAAEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLDIE 230
Query: 213 DFCQRLKEFSEKYS-----VQIYLEPGEAIVTNTTTLNTTVLDISEN-IKNLVIVDSSV- 265
++ + + E ++ +++ +EPG IV N L T V + E K V VD+ +
Sbjct: 231 EYAEAIAEALKELCEGGPDLKLIIEPGRYIVANAGVLLTRVGYVKETGGKTFVGVDAGMN 290
Query: 266 --------EAHVPDYLLYQESATIYPNTGPYTAMVCGRSCLAGDIFGEFHFEKPVKIGDR 317
A+ + + T V G C +GD+F + V+ GD
Sbjct: 291 DLIRPALYGAYHEIVPVNKPGE---GETEKVD--VVGPICESGDVFAKDRELPEVEEGDL 345
Query: 318 ISFEDVAGYN 327
++ D Y
Sbjct: 346 LAIHDAGAYG 355
>gnl|CDD|144023 pfam00278, Orn_DAP_Arg_deC, Pyridoxal-dependent decarboxylase,
C-terminal sheet domain. These pyridoxal-dependent
decarboxylases act on ornithine, lysine, arginine and
related substrates.
Length = 110
Score = 71.5 bits (176), Expect = 3e-13
Identities = 29/110 (26%), Positives = 46/110 (41%), Gaps = 9/110 (8%)
Query: 243 TLNTTVLDISEN--IKNLVIVDSSVEAHVPDYLLYQESATIYP-----NTGPYTAMVCGR 295
TL T V+D+ E + V +D V PD LY I P + + G
Sbjct: 1 TLVTEVIDVKERGDDRKFVYLDDGVYGS-PDPALYDALHPILPVSRLDDEPLRPYTLAGP 59
Query: 296 SCLAGDIFG-EFHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTIAV 344
+C +GD+ + +++GD + F D Y I+ + FNG P +
Sbjct: 60 TCDSGDVLARDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAEVL 109
>gnl|CDD|35841 KOG0622, KOG0622, KOG0622, Ornithine decarboxylase [Amino acid
transport and metabolism].
Length = 448
Score = 57.3 bits (138), Expect = 7e-09
Identities = 74/394 (18%), Positives = 134/394 (34%), Gaps = 44/394 (11%)
Query: 3 KTPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYE 62
K +++ D + L+ + + V+ A+KC + + L G +S E
Sbjct: 55 KQAFFVADLGAIERKLE--AWKKALPRVRPFYAVKCNSDPKVLRLLASLGCGFDCASKNE 112
Query: 63 VMLG-HEKFGGETHAYNVAYKDCE--IDAVLSNCDTIIFNTVSQLNKFKDKAQKLHK--K 117
+ L E Y K A + F+ +L K K H
Sbjct: 113 LDLVLSLGVSPERIIYANPCKQVSQIKYAAKHGVSVMTFDNEEELEKVA----KSHPNAN 168
Query: 118 IGLRINPSVSYSKFILADPNRPFSRLGEKCK---DKIESEIKNVNGLMFH--NNC-ENKS 171
+ LRI S + N F + C+ D + NV G+ FH + C + ++
Sbjct: 169 LLLRIATDDSTA---TCRLNLKFGCSLDNCRHLLDMAKELELNVVGVSFHVGSGCTDLQA 225
Query: 172 FLCFSAMLKNIEKEFGHFITQIEWISLGGGIHFTD-KDYPVKDFCQRLKEFSEKY----S 226
+ + +N+ +++ + +GGG + ++ + + Y
Sbjct: 226 YRDAISDARNVFDMGAELGFEMDILDIGGGFPGDEGHAVVFEEIADVINTALDLYFPSGG 285
Query: 227 VQIYLEPGEAIVTNTTTLNTTVLDISENIKNLVIVDSSVEAHVPDY------------LL 274
V I EPG V + TL V+ E + D + Y +L
Sbjct: 286 VDIIAEPGRFFVASAFTLAVNVIAKKEVDAKKITSDDEDDEVTFMYYVNDGVYGSFNCIL 345
Query: 275 YQESATI-------YPNTGPYTAMVCGRSCLAGDIFGEFHFEKPVKIGDRISFEDVAGYN 327
+ I Y + + G +C D+ E + +GD + FE++ Y
Sbjct: 346 FDHQHPIPLVVKDPSEEEPLYKSSIWGPTCDGLDVIAEDCLLPQLNVGDWLVFENMGAYT 405
Query: 328 INRKNWFNGINMPTIAVKNVDGTIKAIREFSYND 361
++ + FNG P I DG + IR+ D
Sbjct: 406 MSAASTFNGFQRPKIYYVMSDGDWEKIRDAETFD 439
>gnl|CDD|143508 cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme MccE. This subfamily is composed
of uncharacterized proteins with similarity to
Escherichia coli MccE, a hypothetical protein that is
homologous to eukaryotic ornithine decarboxylase (ODC)
and diaminopimelate decarboxylase (DapDC). ODC and DapDC
are fold type III PLP-dependent enzymes that contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Most members
of this subfamily share the same domain architecture as
ODC and DapDC. A few members, including Escherichia coli
MccE, contain an additional acetyltransferase domain at
the C-terminus.
Length = 379
Score = 53.8 bits (130), Expect = 8e-08
Identities = 59/282 (20%), Positives = 109/282 (38%), Gaps = 53/282 (18%)
Query: 89 VLSNCDTIIFNTVSQLNKFKDKAQKLHK--KIGLRINPSVS---YSKFILADPNRPFSRL 143
L N D+ +L + + A++L + K+G+R+N + +S+F
Sbjct: 101 ALINIDSF-----DELERILEIAKELGRVAKVGIRLNMNYGNNVWSRFGF--DIEENGEA 153
Query: 144 GEKCKDKIESEIKNVNGLMFH-----NNCENKSFLCFSAMLKN----IEKEFGHFITQIE 194
K ES+ ++ GL H N E +SA K +++ FG ++E
Sbjct: 154 LAALKKIQESKNLSLVGLHCHVGSNILNPEA-----YSAAAKKLIELLDRLFGL---ELE 205
Query: 195 WISLGGGIHFTDK--------DYPVKDF-------CQRLKEFSEKYSVQ--IYLEPGEAI 237
++ LGGG + V D LKE+ + + LEPG A+
Sbjct: 206 YLDLGGGF-PAKTPLSLAYPQEDTVPDPEDYAEAIASTLKEYYANKENKPKLILEPGRAL 264
Query: 238 VTNTTTLNTTVLDISE-NIKNLVIVDSSVEAHVPDYLLYQESATI---YPNTGPYTA-MV 292
V + L V+ + +N+ + D+ + ++P Y + V
Sbjct: 265 VDDAGYLLGRVVAVKNRYGRNIAVTDAGIN-NIPTIFWYHHPILVLRPGKEDPTSKNYDV 323
Query: 293 CGRSCLAGDIFGEFHFEKPVKIGDRISFEDVAGYNINRKNWF 334
G +C+ D+ P+ +GD ++ +V YN+ + N F
Sbjct: 324 YGFNCMESDVLFPNVPLPPLNVGDILAIRNVGAYNMTQSNQF 365
>gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent
Enzymes. The fold type III PLP-dependent enzyme family
is predominantly composed of two-domain proteins with
similarity to bacterial alanine racemases (AR) including
eukaryotic ornithine decarboxylases (ODC), prokaryotic
diaminopimelate decarboxylases (DapDC), biosynthetic
arginine decarboxylases (ADC), carboxynorspermidine
decarboxylases (CANSDC), and similar proteins. AR-like
proteins contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain. They exist
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. These
proteins play important roles in the biosynthesis of
amino acids and polyamine. The family also includes the
single-domain YBL036c-like proteins, which contain a
single PLP-binding TIM-barrel domain without any N- or
C-terminal extensions. Due to the lack of a second
domain, these proteins may possess only limited D- to
L-alanine racemase activity or non-specific racemase
activity.
Length = 211
Score = 40.8 bits (96), Expect = 6e-04
Identities = 42/192 (21%), Positives = 69/192 (35%), Gaps = 31/192 (16%)
Query: 27 NAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYEVM-LGHEKFGGETHAYNVAYK--- 82
AG+ L +K A + TL G +SL E + L E + K
Sbjct: 13 PAGITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPPEPILFLGPCKQVS 72
Query: 83 DCEIDAVLSNCDTIIFNTVSQLNKFKDKAQKLHKK--IGLRINPSVSYSKFILADPNRPF 140
+ E DA + +++ +L K ++ A K + LRI+ KF +
Sbjct: 73 ELE-DAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRIDTGDENGKFGV------- 124
Query: 141 SRLGEKCKDKIESEIK----NVNGLMFH--NNCENKS-----FLCFSAMLKNIEKEFGHF 189
R E K +E + + GL H + E+ S F A L + +
Sbjct: 125 -RPEE-LKALLERAKELPHLRLVGLHTHFGSADEDYSPFVEALSRFVAALDQLGELGID- 181
Query: 190 ITQIEWISLGGG 201
+E +S+GG
Sbjct: 182 ---LEQLSIGGS 190
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar to
bacterial alanine racemases. They exist 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. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity. Also members of this subfamily are proteins
with homology to ODC but do not possess any catalytic
activity, the Antizyme inhibitor (AZI) and ODC-paralogue
(ODC-p). AZI binds to the regulatory protein Antizyme
with a higher affinity than ODC and prevents ODC
degradation. ODC-p is a novel ODC-like protein, present
only in mammals, that is specifically exressed in the
brain and testes. ODC-p may function as a
tissue-specific antizyme inhibitory protein.
Length = 362
Score = 40.2 bits (95), Expect = 0.001
Identities = 33/182 (18%), Positives = 67/182 (36%), Gaps = 28/182 (15%)
Query: 184 KEFGHFITQIEWISLGGG--IHFTDKDYPVKDFCQRLKEFSEKY----SVQIYLEPGEAI 237
E G +++ + +GGG + ++ + ++Y V+I EPG +
Sbjct: 187 AELGF---KLKLLDIGGGFPGSYDGVVPSFEEIAAVINRALDEYFPDEGVRIIAEPGRYL 243
Query: 238 VTNTTTLNTTVL----DISENIKNLVIVDSSV----------EAHVPDYLLYQESATIYP 283
V + TL V+ ++ + ++ V P +L
Sbjct: 244 VASAFTLAVNVIAKRKRGDDDRERWYYLNDGVYGSFNEILFDHIRYPPRVLKDGGRD--G 301
Query: 284 NTGPYTAMVCGRSCLAGD-IFGEFHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTI 342
P + + G +C + D I+ + + + +GD + FE++ Y + FNG P I
Sbjct: 302 ELYPSS--LWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGAYTTAYASTFNGFPPPKI 359
Query: 343 AV 344
Sbjct: 360 VY 361
>gnl|CDD|33075 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 33.0 bits (75), Expect = 0.13
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 308 FEKPVKIGDRISFEDVAGY 326
FE+PVK+GD ++ V+G
Sbjct: 657 FERPVKVGDTVTIGTVSGT 675
>gnl|CDD|144501 pfam00924, MS_channel, Mechanosensitive ion channel. Two members
of this protein family from M. jannaschii have been
functionally characterized. Both proteins form
mechanosensitive (MS) ion channels upon reconstitution
into liposomes and functional examination by the
patch-clamp technique. Therefore this family are likely
to also be MS channel proteins.
Length = 203
Score = 31.4 bits (72), Expect = 0.41
Identities = 12/19 (63%), Positives = 12/19 (63%)
Query: 308 FEKPVKIGDRISFEDVAGY 326
FEKP KIGD I DV G
Sbjct: 55 FEKPFKIGDWIEIGDVEGT 73
>gnl|CDD|35573 KOG0352, KOG0352, KOG0352, ATP-dependent DNA helicase [Replication,
recombination and repair].
Length = 641
Score = 30.5 bits (68), Expect = 0.68
Identities = 27/116 (23%), Positives = 45/116 (38%), Gaps = 20/116 (17%)
Query: 229 IYLEPGEAIVTNTT--TLNTTVLDISENIKNLVIVDSSVEAHV---------PDYLLYQE 277
+Y+ P E T+ LN + ++ ++VD EAH PDYL
Sbjct: 117 LYITP-EGAATDGFQKLLNGLA---NRDVLRYIVVD---EAHCVSQWGHDFRPDYLTLGS 169
Query: 278 SATIYPNTGPYTAMVCGRSCLAG-DIFGEFHFEKPVKIGDRISFEDVAGYNINRKN 332
++ P P+ A+ + DI + PV I +F D Y+ + K+
Sbjct: 170 LRSVCPGV-PWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMKS 224
>gnl|CDD|146017 pfam03180, Lipoprotein_9, NLPA lipoprotein. This family of
bacterial lipoproteins contains several antigenic
members, that may be involved in bacterial virulence.
Their precise function is unknown. However they are
probably distantly related to pfam00497 which are solute
binding proteins.
Length = 236
Score = 28.0 bits (63), Expect = 4.5
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 240 NTTTLNTTVLDISENIKNLVIVDSSVEA 267
+ L TV DI+EN KNL I + +EA
Sbjct: 126 DGAGLLATVKDITENPKNLKIKE--LEA 151
>gnl|CDD|36534 KOG1320, KOG1320, KOG1320, Serine protease [Posttranslational
modification, protein turnover, chaperones].
Length = 473
Score = 27.6 bits (61), Expect = 5.4
Identities = 16/84 (19%), Positives = 22/84 (26%), Gaps = 9/84 (10%)
Query: 187 GHFITQIEWISLGGGIHFTDKDYPVKDFCQRLKEFSEKYSVQIYLEPGEAIVTNTT---- 242
G ++ I GI F V RL EF L P + +
Sbjct: 319 GVNTRKVTRIGFSHGISFKIPIDTVLVIVLRLGEFQISLRPVKPLVPVHQYIGLPSYYIF 378
Query: 243 -----TLNTTVLDISENIKNLVIV 261
T + LV+V
Sbjct: 379 AGLVFVPLTKSYIFPSGVVQLVLV 402
>gnl|CDD|100009 cd06152, YjgF_YER057c_UK114_like_4, YjgF, YER057c, and UK114 belong
to a large family of proteins present in bacteria,
archaea, and eukaryotes with no definitive function.
The conserved domain is similar in structure to
chorismate mutase but there is no sequence similarity
and no functional connection. Members of this family
have been implicated in isoleucine (Yeo7, Ibm1, aldR)
and purine (YjgF) biosynthesis, as well as threonine
anaerobic degradation (tdcF) and mitochondrial DNA
maintenance (Ibm1). This domain homotrimerizes forming a
distinct intersubunit cavity that may serve as a small
molecule binding site..
Length = 114
Score = 27.3 bits (61), Expect = 7.1
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 13/55 (23%)
Query: 306 FHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTI-------AVKNVDGTIKA 353
H+ + V+IGDRI G++ + +P A NV+ +KA
Sbjct: 1 LHYSQAVRIGDRIEISGQGGWDP------DTGKIPEDLEEEIDQAFDNVELALKA 49
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
0.320 0.137 0.409
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,458,575
Number of extensions: 236775
Number of successful extensions: 643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 622
Number of HSP's successfully gapped: 23
Length of query: 367
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 272
Effective length of database: 4,210,882
Effective search space: 1145359904
Effective search space used: 1145359904
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: 58 (26.1 bits)