RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780765|ref|YP_003065178.1| 3-deoxy-manno-octulosonate
cytidylyltransferase [Candidatus Liberibacter asiaticus str. psy62]
(268 letters)
>gnl|CDD|180091 PRK05450, PRK05450, 3-deoxy-manno-octulosonate
cytidylyltransferase; Provisional.
Length = 245
Score = 305 bits (784), Expect = 9e-84
Identities = 119/249 (47%), Positives = 148/249 (59%), Gaps = 15/249 (6%)
Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQA 68
K L+IIPAR S R P K LADI G PMI+ RA KA RV+VA DD +I + V
Sbjct: 2 KFLIIIPARYASTRLPGKPLADIGGKPMIVRVYERASKAGADRVVVATDDERIADAVEAF 61
Query: 69 GFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPI 128
G E VMT H SG+DRI EA + I+VN+Q D P I PEI+ V PL NP
Sbjct: 62 GGEVVMTSPDHPSGTDRIAEAAAKLGLADD-DIVVNVQGDEPLIPPEIIDQVAEPLANPE 120
Query: 129 VDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHG--------TGPF 180
D+ TL IH + + +PN+VK+V+ + +G RALYF+R P+G P
Sbjct: 121 ADMATLAVPIHDAEEAFNPNVVKVVLDA---DG--RALYFSRAPIPYGRDAFADSAPTPV 175
Query: 181 YQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAM-SVDTTN 239
Y+H+GIYAYRR L+RF L PS LE+ ESLEQLRALE RI V +V+ VDT
Sbjct: 176 YRHIGIYAYRRGFLRRFVSLPPSPLEKIESLEQLRALENGYRIHVVVVEEAPSIGVDTPE 235
Query: 240 DLEKVRTLI 248
DLE+VR L+
Sbjct: 236 DLERVRALL 244
>gnl|CDD|184007 PRK13368, PRK13368, 3-deoxy-manno-octulosonate
cytidylyltransferase; Provisional.
Length = 238
Score = 217 bits (555), Expect = 2e-57
Identities = 103/243 (42%), Positives = 143/243 (58%), Gaps = 15/243 (6%)
Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKA-NIGRVIVAVDDTKINEIVLQ 67
KV+V+IPAR S R P K L DI G PMI H RA +A + V VA DD +I + V
Sbjct: 2 KVVVVIPARYGSSRLPGKPLLDILGKPMIQHVYERAAQAAGVEEVYVATDDQRIEDAVEA 61
Query: 68 AGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPE-ILASVLLPLQN 126
G + VMT H SG+DR+ E + I++D I +N+Q D P I P I + L +
Sbjct: 62 FGGKVVMTSDDHLSGTDRLAEVMLKIEAD----IYINVQGDEPMIRPRDIDTLIQPMLDD 117
Query: 127 PIVDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHG-TGPF---YQ 182
P +++ TL I + + PN+VK+VV +NG ALYF+R+ P G +
Sbjct: 118 PSINVATLCAPISTEEEFESPNVVKVVV---DKNG--DALYFSRSPIPSRRDGESARYLK 172
Query: 183 HLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDTTNDLE 242
H+GIYA+RR+ L++F+QL + LEQ ESLEQLRALE +I + V + ++ VDT DLE
Sbjct: 173 HVGIYAFRRDVLQQFSQLPETPLEQIESLEQLRALEHGEKIRMVEVAATSIGVDTPEDLE 232
Query: 243 KVR 245
+VR
Sbjct: 233 RVR 235
>gnl|CDD|129558 TIGR00466, kdsB, 3-deoxy-D-manno-octulosonate cytidylyltransferase.
Length = 238
Score = 181 bits (460), Expect = 2e-46
Identities = 92/244 (37%), Positives = 126/244 (51%), Gaps = 18/244 (7%)
Query: 11 LVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQAGF 70
+VIIPARL S R P K L DI G PMI+H A A ++ R IVA DD + + + G
Sbjct: 1 MVIIPARLASSRLPGKPLEDIFGKPMIVHVAENANESGADRCIVATDDESVAQTCQKFGI 60
Query: 71 ESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVD 130
E MT H SG++R+ E + + + K + IVN+Q D P I EI+ V L V
Sbjct: 61 EVCMTSKHHNSGTERLAEVVEKL-ALKDDERIVNLQGDEPFIPKEIIRQVADNLATKNVP 119
Query: 131 IGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPH-----------GTGP 179
+ L +IH + + +PN VK+V+ S ALYF+R+ P
Sbjct: 120 MAALAVKIHDAEEAFNPNAVKVVLDSQG-----YALYFSRSLIPFDRDFFAKRQTPVGDN 174
Query: 180 FYQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQS-NAMSVDTT 238
+H+GIY YR ++ + P VLE+ E LEQLR L +I VKI Q ++ VDT
Sbjct: 175 LLRHIGIYGYRAGFIEEYVAWKPCVLEEIEKLEQLRVLYYGEKIHVKIAQEVPSVGVDTQ 234
Query: 239 NDLE 242
DLE
Sbjct: 235 EDLE 238
>gnl|CDD|178505 PLN02917, PLN02917, CMP-KDO synthetase.
Length = 293
Score = 144 bits (364), Expect = 2e-35
Identities = 96/251 (38%), Positives = 133/251 (52%), Gaps = 17/251 (6%)
Query: 7 KEKVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKA-NIGRVIVAVDDTKINEIV 65
+ +V+ IIPAR S RF K L I G PMI T RA+ A + ++VA DD +I E
Sbjct: 45 RSRVVGIIPARFASSRFEGKPLVHILGKPMIQRTWERAKLATTLDHIVVATDDERIAECC 104
Query: 66 LQAGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQ 125
G + +MT S ++G++R EAL ++ KK I+VN+Q D P IEPEI+ V+ LQ
Sbjct: 105 RGFGADVIMTSESCRNGTERCNEALKKLE--KKYDIVVNIQGDEPLIEPEIIDGVVKALQ 162
Query: 126 -NPIVDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHGTG------ 178
P T T + D DPN VK VV G A+YF+R P+
Sbjct: 163 AAPDAVFSTAVTSLK-PEDASDPNRVKCVV---DNQG--YAIYFSRGLIPYNKSGKVNPQ 216
Query: 179 -PFYQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDT 237
P+ HLGI +Y + LK + +L P+ L+ E LEQL+ LE ++ V V A VDT
Sbjct: 217 FPYLLHLGIQSYDAKFLKIYPELPPTPLQLEEDLEQLKVLENGYKMKVIKVDHEAHGVDT 276
Query: 238 TNDLEKVRTLI 248
D+EK+ L+
Sbjct: 277 PEDVEKIEALM 287
>gnl|CDD|163336 TIGR03584, PseF, pseudaminic acid CMP-transferase. The sequences
in this family include the pfam02348
(cytidyltransferase) domain and are homologous to the
NeuA protein responsible for the transfer of CMP to
neuraminic acid. According to, this gene is responsible
for the transfer of CMP to the structurally related
sugar, pseudaminic acid which is observed as a
component of sugar modifications of flagellin in
Campylobacter species. This gene is commonly observed
in apparent operons with other genes responsible for
the biosynthesis of pseudaminic acid and as a component
of flagellar and exopolysaccharide biosynthesis loci.
Length = 222
Score = 44.2 bits (105), Expect = 3e-05
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 11 LVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANI-GRVIVAVDDTKINEIVLQAG 69
+ IIPAR S R P+K + G PMI ++ A + + +V+V+ DD +I E+ G
Sbjct: 1 IAIIPARGGSKRIPRKNIKPFCGKPMIAYSIEAALNSGLFDKVVVSTDDEEIAEVAKSYG 60
>gnl|CDD|184642 PRK14353, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 446
Score = 32.5 bits (75), Expect = 0.13
Identities = 34/144 (23%), Positives = 48/144 (33%), Gaps = 39/144 (27%)
Query: 21 MRFPK-KILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQAGFESVMTHTSH 79
M+ K+L + G PM+ H A RV V V+ G E+V +
Sbjct: 19 MKSSLPKVLHPVAGRPMLAHVLAAAASLGPSRVAV----------VVGPGAEAVAAAAAK 68
Query: 80 QSGSDRIF----------------EALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLP 123
+ IF EAL D ++ + D P I E LA +
Sbjct: 69 IAPDAEIFVQKERLGTAHAVLAAREALAGGYGD-----VLVLYGDTPLITAETLARLRER 123
Query: 124 LQNPIVDIGTLGTRIHGSTDPDDP 147
L + D+ LG R DP
Sbjct: 124 LADG-ADVVVLGFR------AADP 140
>gnl|CDD|131935 TIGR02889, spore_YpeB, germination protein YpeB. Members of this
family are YpeB, a protein usually encoded with the
putative spore-cortex-lytic enzyme SleB and required,
together with SleB, for normal germination. This family
is retricted to endospore-forming species in the
Firmicutes lineage of bacteria, and found in all such
species to date except Clostridium perfringens. The
matching phenotypes of mutants in SleB (called a lytic
transglycosylase) and YpeB suggests that YpeB is
necessary to allow SleB to function.
Length = 435
Score = 28.5 bits (64), Expect = 1.9
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 176 GTGPFYQHLGIYAY---RREALKRFTQLSPSVLEQRESL-EQLRALEARMRIDVKIVQSN 231
T F +G + Y ++A + LS + +L Q LE ++R IV
Sbjct: 97 KTSKFLSQVGDFTYTLSVKDAEGK--SLSDKEYKTLTTLYNQAVKLENQLRKVQNIVMQG 154
Query: 232 AM 233
+
Sbjct: 155 GV 156
>gnl|CDD|184034 PRK13405, bchH, magnesium chelatase subunit H; Provisional.
Length = 1209
Score = 27.7 bits (62), Expect = 3.0
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 12/72 (16%)
Query: 191 REALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDTTND---------L 241
+ +L+R+ L P E+R L L +A V + + + L
Sbjct: 678 KASLERWRGLPPDATEERAELAALIQAQAA---AVDLAPAEPAWEEEAGARIAKLWAALL 734
Query: 242 EKVRTLIPHDHH 253
E TLIPH H
Sbjct: 735 ELEYTLIPHGLH 746
>gnl|CDD|178905 PRK00155, ispD, 2-C-methyl-D-erythritol 4-phosphate
cytidylyltransferase; Reviewed.
Length = 227
Score = 27.4 bits (62), Expect = 3.6
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 7 KEKVLVIIPA-----RLNSMRFPKKILADINGLPMILHTAIRARKAN--IGRVIVAV--D 57
V IIPA R+ + R K + G P++ HT + A A+ I +IV V D
Sbjct: 1 MMMVYAIIPAAGKGSRMGADR--PKQYLPLGGKPILEHT-LEAFLAHPRIDEIIVVVPPD 57
Query: 58 DTK 60
D
Sbjct: 58 DRP 60
>gnl|CDD|132513 TIGR03473, HpnK, hopanoid biosynthesis associated protein HpnK.
The sequences represented by this model are members of
the pfam04794 "YdjC-like" family of uncharacterized
proteins. The member of this clade from
Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0976) is
found in the same locus as squalene-hopene cyclase
(SHC, TIGR01507) and other genes associated with the
biosynthesis of hopanoid natural products. Similarly,
in Ralstonia eutropha JMP134 (Reut_B4902) this gene is
adjacent to HpnAB, IspH and HpnH (TIGR03470), although
SHC itself is elsewhere in the genome. Notably, this
gene (here named HpnK) and three others form a
conserved set (HpnIJKL) which occur in a subset of all
genomes containing the SHC enzyme. This relationship
was discerned using the method of partial phylogenetic
profiling. This group includes Zymomonas mobilis, the
organism where the initial hopanoid biosynthesis locus
was described consisting of the genes HpnA-E and SHC
(HpnF). Continuing past SHC are found a phosphorylase
enzyme (ZMO0873, i.e. HpnG, TIGR03468) and a radical
SAM enzyme (ZMO0874), HpnH. Although discontinuous in
Z. mobilis, we continue the gene symbol sequence with
HpnIJKL.
Length = 283
Score = 27.4 bits (61), Expect = 4.1
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 51 RVIVAVDD----TKINEIVLQAGFESVMTHTSHQSGSDRIFEA 89
R+IV DD ++NE V +A + ++T S G+ +A
Sbjct: 3 RLIVTADDFGLSLEVNEAVEKAHRDGILTAASLMVGAPAAEDA 45
>gnl|CDD|172940 PRK14465, PRK14465, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 342
Score = 27.2 bits (60), Expect = 4.4
Identities = 14/34 (41%), Positives = 17/34 (50%)
Query: 185 GIYAYRREALKRFTQLSPSVLEQRESLEQLRALE 218
G+Y R E +FT S V E+ E L L LE
Sbjct: 35 GLYVNRYETWDQFTTFSKEVKEKLEELCSLTELE 68
>gnl|CDD|184643 PRK14354, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 458
Score = 27.1 bits (61), Expect = 4.6
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 26 KILADINGLPMILHTAIRARKANIGRVIVAV 56
K+L + G PM+ H +KA I +++ V
Sbjct: 22 KVLHKVCGKPMVEHVVDSVKKAGIDKIVTVV 52
>gnl|CDD|180612 PRK06543, PRK06543, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 281
Score = 27.1 bits (60), Expect = 5.0
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 28 LADINGLPMILHTAIRARKANIG---RVIVAVDDTKINEIVLQAGFESVM 74
LA + + L A+R +A +G V V VD E VL AG +++M
Sbjct: 169 LAALAAQGLDLTEALRHVRAQLGHTTHVEVEVDRLDQIEPVLAAGVDTIM 218
>gnl|CDD|152291 pfam11855, DUF3375, Protein of unknown function (DUF3375). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 479 to 499 amino acids in
length.
Length = 471
Score = 26.6 bits (59), Expect = 7.1
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 192 EALKRFTQLSPSVLEQRESLEQLRALEAR 220
E+L+RF S + LE R ++ LR E+
Sbjct: 302 ESLRRFVD-SQTWLENRRVMQLLREAESL 329
>gnl|CDD|152494 pfam12059, DUF3540, Protein of unknown function (DUF3540). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 212 to 238 amino acids in length.
This protein has a conserved SCL sequence motif.
Length = 195
Score = 26.6 bits (59), Expect = 8.0
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 195 KRFTQLSPSVLEQRESLEQLRALEARMRID 224
R TQ + + E +Q+RA +
Sbjct: 138 DRLTQRAKNSFRTVEGTDQVRAGNLDQTAE 167
>gnl|CDD|162797 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3
family of metallopeptidases contains several distinct
clades. Oligoendopeptidase F as characterized in
Lactococcus, the functionally equivalent
oligoendopeptidase B of group B Streptococcus, and
closely related sequences are described by TIGR00181.
The present family is quite similar but forms a distinct
clade, and a number of species have one member of each.
A greater sequence difference separates members of
TIGR02289, probable oligoendopeptidases of the M3 family
that probably should not be designated PepF.
Length = 587
Score = 26.1 bits (58), Expect = 8.8
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 184 LGIYAYRREALKRFTQLSPSVLEQ--RESLEQL 214
LG+YA RE + F ++L + E+L
Sbjct: 524 LGLYAKYREEGESFVPKYIALLRDTGSMTPEEL 556
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
0.320 0.136 0.383
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,429,852
Number of extensions: 289125
Number of successful extensions: 670
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 29
Length of query: 268
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 176
Effective length of database: 4,006,537
Effective search space: 705150512
Effective search space used: 705150512
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: 56 (25.3 bits)