RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|255764473|ref|YP_003064846.2| ornithine carbamoyltransferase
[Candidatus Liberibacter asiaticus str. psy62]
(306 letters)
>gnl|CDD|30427 COG0078, ArgF, Ornithine carbamoyltransferase [Amino acid transport
and metabolism].
Length = 310
Score = 407 bits (1048), Expect = e-114
Identities = 157/310 (50%), Positives = 205/310 (66%), Gaps = 7/310 (2%)
Query: 1 MMTYPKHFADLSNISSSNLSCIIEVAKKIKNSSENIFENKPLSGKVLAMIFEKPSTRTRV 60
+HF L + + L ++++A ++K + + E K GK LA+IFEK STRTRV
Sbjct: 2 SNLAGRHFLSLLDFTPEELEALLDLAAELKAAKKAGKELKL-KGKNLALIFEKTSTRTRV 60
Query: 61 SFEVAMKHLGGDTIFLSGSEMQLGRAETIGDTAKVLSRYVDAIVMRTTNHSRLLELTEYA 120
SFEVA LGG I+L + QLGR E+I DTA+VLSR VDAI++R +H L EL +Y+
Sbjct: 61 SFEVAATQLGGHAIYLGPGDSQLGRGESIKDTARVLSRMVDAIMIRGFSHETLEELAKYS 120
Query: 121 TVPVINALTDNTHPCQIIADIMTFEEHRGSVKGKLFSWSGDGNNILHSLIEGAARFNYLL 180
VPVIN LTD HPCQ +AD+MT +EH GS+KG ++ GDGNN+ +SL+ AA+ +
Sbjct: 121 GVPVINGLTDEFHPCQALADLMTIKEHFGSLKGLKLAYVGDGNNVANSLLLAAAKLGMDV 180
Query: 181 NIATPIGSEPRNEYLNWARNQ----GASVALFHDAVQAVKGAHCVFTDTWISMNQEFKAR 236
IATP G EP E + A+ G + L D +AVKGA V+TD W+SM +E +A
Sbjct: 181 RIATPKGYEPDPEVVEKAKENAKESGGKITLTEDPEEAVKGADVVYTDVWVSMGEEAEAE 240
Query: 237 EEHV--FQPFQVNLSLMSMAHPDALFMHCLPAHRGEEVINEVLDGPQSVVFDEAENRLHT 294
E + P+QVN LM++A PDA+FMHCLPAHRGEEV +EV +GP SVVFDEAENRLHT
Sbjct: 241 ERRIAFLPPYQVNEELMALAGPDAIFMHCLPAHRGEEVTDEVFEGPASVVFDEAENRLHT 300
Query: 295 QKAILLWCFG 304
QKA+L G
Sbjct: 301 QKAVLAALLG 310
>gnl|CDD|36717 KOG1504, KOG1504, KOG1504, Ornithine carbamoyltransferase OTC/ARG3
[Amino acid transport and metabolism].
Length = 346
Score = 288 bits (739), Expect = 1e-78
Identities = 133/304 (43%), Positives = 182/304 (59%), Gaps = 9/304 (2%)
Query: 5 PKHFADLSNISSSNLSCIIEVAKKIKN--SSENIFENKPLSGKVLAMIFEKPSTRTRVSF 62
+ + + S+ + +++ A ++K PL GK +AMIF K STRTRVS
Sbjct: 39 LRDLLSIKDFSTEEIKTLLDRASEVKALLKQNGERNYLPLKGKSMAMIFAKRSTRTRVST 98
Query: 63 EVAMKHLGGDTIFLSGSEMQLGRAETIGDTAKVLSRYVDAIVMRTTNHSRLLELTEYATV 122
E LGG +FL +++QLG E++ DTA+VLS VD I+ R HS +L L +Y++V
Sbjct: 99 ETGFFLLGGHPMFLGKNDIQLGVNESLYDTARVLSSMVDIIMARVNKHSDILTLAKYSSV 158
Query: 123 PVINALTDNTHPCQIIADIMTFEEHRG-SVKGKLFSWSGDGNNILHSLIEGAARFNYLLN 181
P+IN L D+ HP QI+AD++T EH G SV+G +W GDGNN+LHS + AA+F +
Sbjct: 159 PIINGLCDHFHPLQILADLLTIIEHFGKSVEGLKVAWIGDGNNVLHSWMIAAAKFGIHFS 218
Query: 182 IATPIGSEPRNEYLN----WARNQGASVALFHDAVQAVKGAHCVFTDTWISMNQEFKARE 237
ATP G EP + ++ A G+ L +D ++AV GA+ + TDTWISM QE +
Sbjct: 219 CATPKGYEPDKDIVSKAKQAAEENGSKFELTNDPLEAVIGANVLVTDTWISMGQEDEKEA 278
Query: 238 E-HVFQPFQVNLSLMSMAHPDALFMHCLPAHRGEEVINEVLDGPQSVVFDEAENRLHTQK 296
FQ FQV LM +A P A FMHCLP H EEV +EV GP S+VF EAENR Q
Sbjct: 279 RLKAFQGFQVTEELMKVAGPKAKFMHCLPRHP-EEVSDEVFYGPYSIVFPEAENRKWAQM 337
Query: 297 AILL 300
A++L
Sbjct: 338 AVML 341
>gnl|CDD|145728 pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase,
carbamoyl-P binding domain.
Length = 140
Score = 194 bits (496), Expect = 3e-50
Identities = 65/143 (45%), Positives = 93/143 (65%), Gaps = 4/143 (2%)
Query: 6 KHFADLSNISSSNLSCIIEVAKKIKNSSENIFEN-KPLSGKVLAMIFEKPSTRTRVSFEV 64
+H L ++S L ++++A ++K + L GK LA++F +PSTRTR+SFE
Sbjct: 1 RHLLSLDDLSREELEALLDLAAELK---KKPRSGSPLLRGKTLALLFFEPSTRTRLSFEA 57
Query: 65 AMKHLGGDTIFLSGSEMQLGRAETIGDTAKVLSRYVDAIVMRTTNHSRLLELTEYATVPV 124
A K LGG I+L LG+ E++ DTA+VLSRYVDAIV+R +H L EL +Y++VPV
Sbjct: 58 AAKRLGGHVIYLDPGSSSLGKGESLKDTARVLSRYVDAIVIRHPSHGALEELAKYSSVPV 117
Query: 125 INALTDNTHPCQIIADIMTFEEH 147
INA D+ HP Q +AD++T EH
Sbjct: 118 INAGDDHEHPTQALADLLTIREH 140
>gnl|CDD|143948 pfam00185, OTCace, Aspartate/ornithine carbamoyltransferase,
Asp/Orn binding domain.
Length = 155
Score = 165 bits (421), Expect = 1e-41
Identities = 62/158 (39%), Positives = 88/158 (55%), Gaps = 10/158 (6%)
Query: 152 KGKLFSWSGDG--NNILHSLIEGAARFNYLLNIATPIGSEPRNEYLNWAR-----NQGAS 204
G + GDG N + HSLI A+F + + P G P E ++ A+ + G S
Sbjct: 1 DGLKVAIVGDGKHNRVAHSLILALAKFGMEVVLVAPKGLPPDPELVDEAKKNALKSGGIS 60
Query: 205 VALFHDAVQAVKGAHCVFTDTWISMNQEFKAREEHVFQPFQVNLSLMSMAHPDALFMHCL 264
+ + D +A+KGA V+TD W E + R E +QV L+ A PDA+ MH L
Sbjct: 61 ITVTDDLEEALKGADVVYTDRWQK---EREERLEEFKPDYQVTAELLKKAKPDAIVMHPL 117
Query: 265 PAHRGEEVINEVLDGPQSVVFDEAENRLHTQKAILLWC 302
PAHRGEE+ ++V DGP+SV+FD+AEN LH + A+L
Sbjct: 118 PAHRGEEITDDVDDGPRSVIFDQAENGLHVRMALLALL 155
>gnl|CDD|30886 COG0540, PyrB, Aspartate carbamoyltransferase, catalytic chain
[Nucleotide transport and metabolism].
Length = 316
Score = 163 bits (414), Expect = 6e-41
Identities = 97/311 (31%), Positives = 149/311 (47%), Gaps = 18/311 (5%)
Query: 1 MMTYPKHFADLSNISSSNLSCIIEVAKKIKNSSENIFENKPLSGKVLAMIFEKPSTRTRV 60
+H + ++S L +++ A + K + + L GKV+A +F +PSTRTR+
Sbjct: 3 NPFKMRHLISIEDLSREELELLLDTADEFKAVARAEKKLDLLKGKVVANLFFEPSTRTRL 62
Query: 61 SFEVAMKHLGGDTIFLSGSEMQLGRAETIGDTAKVLSRY-VDAIVMRTTNHSRLLELTEY 119
SFE AMK LG D + S SE + ET+ DT + LS Y VDAIV+R L E+
Sbjct: 63 SFETAMKRLGADVVNFSDSESSSKKGETLADTIRTLSAYGVDAIVIRHPEEGAARLLAEF 122
Query: 120 ATV-PVINALTD--NTHPCQIIADIMTFEEHRGSVKGKLFSWSGDGNN--ILHSLIEGAA 174
+ V PVINA D + HP Q + D+ T E G + G + GD + + HS I+
Sbjct: 123 SGVNPVINA-GDGSHQHPTQALLDLYTIREEFGRLDGLKIAIVGDLKHSRVAHSNIQALK 181
Query: 175 RFNYLLNIATPIGSEPRNEYLNWARNQGASVALFHDAVQAVKGAHCVFTDTWIS---MNQ 231
RF + + +P P L +G V + ++ A ++ + N
Sbjct: 182 RFGAEVYLVSPETLLPPEYILEELEEKGGVVVEHDSDEEVIEEADVLYM-LRVQKERFND 240
Query: 232 EF---KAREEHVFQPFQVNLSLMSMAHPDALFMHCLPAHRGEEVINEVLDGPQSVVFDEA 288
K +E + L+L +A PDA+ MH LP +R E+ +EV D PQS F +
Sbjct: 241 PEEYSKVKEYYKLY----GLTLERLAKPDAIVMHPLPVNRVVEIASEVDDTPQSRYFQQV 296
Query: 289 ENRLHTQKAIL 299
+N + + A+L
Sbjct: 297 KNGVAVRMALL 307
>gnl|CDD|35591 KOG0370, KOG0370, KOG0370, Multifunctional pyrimidine synthesis
protein CAD (includes carbamoyl-phophate synthetase,
aspartate transcarbamylase, and glutamine
amidotransferase) [General function prediction only].
Length = 1435
Score = 35.7 bits (82), Expect = 0.019
Identities = 16/144 (11%), Positives = 40/144 (27%), Gaps = 8/144 (5%)
Query: 22 IIEVAKKIKNSSENIFENKPLSGKVLAMIFEKPSTRTRVSFEVAMKH-LGGDTIFLSGSE 80
I+ A + N+ ++ + + + ++ E ++K + + +
Sbjct: 537 IVRAAYALGGLGSGFANNE---EELQDLAAQALALSPQILVEKSLKGWKEVEYEVVRDAY 593
Query: 81 MQLGRA--ETIGDTAKVLSRYVDAIVMRTTNHSRLLELTEYATVPVINAL-TDNTHPCQI 137
D + + + T ++ + VI L Q
Sbjct: 594 DNCITVCNMENFDPLGIHTGDSIVVAPSQTLSDEEYQMLRTTAIKVIRHLGVVGECNIQY 653
Query: 138 IADIMTFEEHRGSVKGKLFSWSGD 161
+ + E V +L S S
Sbjct: 654 ALNPYSLEYRIIEVNARL-SRSSA 676
>gnl|CDD|133078 cd03867, M14_CPZ, Peptidase M14-like domain of carboxypeptidase
(CP) Z (CPZ), CPZ belongs to the N/E subfamily of the
M14 family of metallocarboxypeptidases (MCPs). The M14
family are zinc-binding CPs which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. CPZ is
a secreted Zn-dependent enzyme whose biological function
is largely unknown. Unlike other members of the N/E
subfamily, CPZ has a bipartite structure, which consists
of an N-terminal cysteine-rich domain (CRD) whose
sequence is similar to Wnt-binding proteins, and a
C-terminal CP catalytic domain that removes C-terminal
Arg residues from substrates. CPZ is enriched in the
extracellular matrix and is widely distributed during
early embryogenesis. That the CRD of CPZ can bind to
Wnt4 suggests that CPZ plays a role in Wnt signaling.
Length = 395
Score = 28.7 bits (64), Expect = 2.0
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 20/83 (24%)
Query: 144 FEEHRGSVKGKL-FSWSGDGNNILHSLIEGAARFNYL----LNIATPIGSE---PRNE-Y 194
F + G + G +S+SG G + FNYL + +G + P E Y
Sbjct: 251 FHKRGGIINGAEWYSFSG-----------GMSDFNYLHTNCFEVTVELGCDKFPPEEELY 299
Query: 195 LNWARNQGASVALFHDAVQAVKG 217
W N+ A ++ + +KG
Sbjct: 300 TIWQENKEALLSFMEMVHRGIKG 322
>gnl|CDD|35512 KOG0291, KOG0291, KOG0291, WD40-repeat-containing subunit of the
18S rRNA processing complex [RNA processing and
modification].
Length = 893
Score = 28.8 bits (64), Expect = 2.2
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 141 IMTFEEHRGSVKGKLFSWSGDGNNILHSLIEGAAR 175
+TF EH V ++ GN +L S ++G R
Sbjct: 385 FVTFTEHTSGVTA--VQFTARGNVLLSSSLDGTVR 417
>gnl|CDD|35737 KOG0517, KOG0517, KOG0517, Beta-spectrin [Cytoskeleton].
Length = 2473
Score = 28.0 bits (62), Expect = 3.5
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 281 QSVVFDEAENR--LHTQKAILLWC 302
Q + + +NR + A+LLWC
Sbjct: 153 QDISIETEDNRETRSAKDALLLWC 176
>gnl|CDD|107314 cd06319, PBP1_ABC_sugar_binding_like_10, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 277
Score = 26.7 bits (59), Expect = 7.4
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 94 KVLSRYVDAIVMRTTNHSR---LLELTEYATVPVINA 127
+ + V I++ TN S LL+L A +PV+ A
Sbjct: 50 TAIDKGVSGIIISPTNSSAAVTLLKLAAQAKIPVVIA 86
>gnl|CDD|107268 cd06273, PBP1_GntR_like_1, This group includes the ligand-binding
domain of putative DNA transcription repressors which
are highly similar to that of the repressor specific for
gluconate (GntR), a member of the LacI-GalR family of
bacterial transcription regulators. This group includes
the ligand-binding domain of putative DNA transcription
repressors which are highly similar to that of the
repressor specific for gluconate (GntR), a member of the
LacI-GalR family of bacterial transcription regulators.
The LacI-GalR family repressors are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 268
Score = 26.8 bits (60), Expect = 7.9
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 61 SFEVAM-KHLGGDTIFLSGSEMQLGRAETIGDTAKVLSRYVDAIVMRTTNHS-RLLELTE 118
+F+ + H G T+ ++ S L R K+L R VD + + +HS LL+L
Sbjct: 20 AFQETLAAH--GYTLLVASSGYDLDREYAQ--ARKLLERGVDGLALIGLDHSPALLDLLA 75
Query: 119 YATVPVINALT---DNTHPC 135
VP + D+ +PC
Sbjct: 76 RRGVPYVATWNYSPDSPYPC 95
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is
a large multi-subunit complex responsible for the
synthesis of all RNAs in the cell. The relative
positioning of the RNAP core is highly conserved between
archaeal RNAP and the three classes of eukaryotic RNAPs.
In archaea, the largest subunit is split into two
polypeptides, A' and A'', which are encoded by separate
genes in an operon. Sequence alignments reveal that the
archaeal A'' subunit corresponds to the C-terminal
one-third of the RNAPII largest subunit (Rpb1). In
subunit A'', several loops in the jaw domain are
shorter. The RNAPII Rpb1 interacts with the
second-largest subunit (Rpb2) to form the DNA entry and
RNA exit channels in addition to the catalytic center of
RNA synthesis.
Length = 363
Score = 26.8 bits (60), Expect = 8.3
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 52 EKPSTRTRVSFEVAMKHL 69
EKPS R +FEV +KHL
Sbjct: 308 EKPSVLARAAFEVTVKHL 325
>gnl|CDD|111344 pfam02438, Adeno_100, Late 100kD protein. The late 100kD protein
is a non-structural viral protein involved in the
transport of hexon from the cytoplasm to the nucleus.
Length = 583
Score = 26.5 bits (59), Expect = 9.0
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 162 GNNILHSLIEGAARFNYLL 180
N +LHS +EG R +Y+
Sbjct: 290 NNPVLHSTLEGEDRRDYIR 308
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 0.133 0.396
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,569,578
Number of extensions: 179925
Number of successful extensions: 402
Number of sequences better than 10.0: 1
Number of HSP's gapped: 389
Number of HSP's successfully gapped: 17
Length of query: 306
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 213
Effective length of database: 4,254,100
Effective search space: 906123300
Effective search space used: 906123300
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: 57 (25.8 bits)