RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022651
(294 letters)
>gnl|CDD|178408 PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
Length = 211
Score = 321 bits (826), Expect = e-112
Identities = 139/218 (63%), Positives = 173/218 (79%), Gaps = 8/218 (3%)
Query: 67 EAIFQKKRSLRSKIRKDLKNMDPIQRSQEDTAVQDIVLESSWFKASRNICAYISCASLRE 126
+ I ++K++LR ++R+ LK + P QR+QED A+Q +LE WFK+S+ +CAY+SCA LRE
Sbjct: 1 DEIREQKKALRKEVRRALKALSPEQRAQEDAAIQSRLLELPWFKSSKRLCAYVSCAKLRE 60
Query: 127 VDTSRIVSEILSNQTDGNGQMRKKLYVPRVEDKNSNMRMLKISAV-KDLVANSMNILEPS 185
VDTS+I+SEIL N K+LYVPRVEDKNSNMRML I+ + DLVANSMNILEP+
Sbjct: 61 VDTSKILSEILQNP-------DKRLYVPRVEDKNSNMRMLHITDMADDLVANSMNILEPT 113
Query: 186 LLDSDGNQCEDVMQASEPVDLLILPGLAFDRSGGRLGRGGGYYDVFLKKYQKLAQEQKWK 245
+D+DGN EDV+QA EP+DLL+LPGLAFDRSG RLGRGGGYYD FL KYQ+LA+E+ WK
Sbjct: 114 PVDADGNPREDVLQAPEPLDLLLLPGLAFDRSGRRLGRGGGYYDTFLSKYQELAKEKGWK 173
Query: 246 QPLLVALLYSLQLVDEESIPVTPYDVPVDALVSPRGFI 283
QPLLVAL YS Q++DE S+PV DV VDALV+P G I
Sbjct: 174 QPLLVALSYSPQILDEGSVPVDETDVLVDALVTPSGVI 211
>gnl|CDD|233985 TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.
This enzyme, 5,10-methenyltetrahydrofolate synthetase,
is also called 5-formyltetrahydrofolate cycloligase.
Function of bacterial proteins in this family was
inferred originally from the known activity of
eukaryotic homologs. Recently, activity was shown
explicitly for the member from Mycoplasma pneumonia.
Members of this family from alpha- and
gamma-proteobacteria, designated ygfA, are often found
in an operon with 6S structural RNA, and show a similar
pattern of high expression during stationary phase. The
function may be to deplete folate to slow 1-carbon
biosynthetic metabolism [Central intermediary
metabolism, One-carbon metabolism].
Length = 179
Score = 134 bits (340), Expect = 5e-39
Identities = 67/209 (32%), Positives = 106/209 (50%), Gaps = 32/209 (15%)
Query: 73 KRSLRSKIRKDLKNMDPIQRSQEDTAVQDIVLESSWFKASRNICAYISCASLR-EVDTSR 131
K+ LR K+ + K + +R +A+ +L +K ++ I Y+ LR EVDT
Sbjct: 1 KKELRKKLLEARKALSSAERKAASSAIAKRLLALIEWKNAKTIALYLP---LRGEVDTRP 57
Query: 132 IVSEILSNQTDGNGQMRKKLYVPRVEDKNSNMRMLKI-SAVKDLVANSMNILEPSLLDSD 190
++ ++L K++ +P+V+ M +I S + L ILEP
Sbjct: 58 LIEQLLKEG--------KRVALPKVDGDGKEMLFFRIWSPEQPLTKGPFGILEP-----V 104
Query: 191 GNQCEDVMQASEPVDLLILPGLAFDRSGGRLGRGGGYYDVFLKKYQKLAQEQKWKQPLLV 250
G+ E V + +DL+I+PG+AFDR G RLG GGGYYD FL + + + +
Sbjct: 105 GDLEEPV--PPDEIDLIIVPGVAFDRRGYRLGYGGGYYDRFLARLKGIT----------I 152
Query: 251 ALLYSLQLVDEESIPVTPYDVPVDALVSP 279
L + QLVDE +P P+DVPVDA+++
Sbjct: 153 GLAFDFQLVDE--LPREPHDVPVDAIITE 179
>gnl|CDD|216717 pfam01812, 5-FTHF_cyc-lig, 5-formyltetrahydrofolate cyclo-ligase
family. 5-formyltetrahydrofolate cyclo-ligase or
methenyl-THF synthetase EC:6.3.3.2 catalyzes the
interchange of 5-formyltetrahydrofolate (5-FTHF) to
5-10-methenyltetrahydrofolate, this requires ATP and
Mg2+. 5-FTHF is used in chemotherapy where it is
clinically known as Leucovorin.
Length = 182
Score = 128 bits (324), Expect = 1e-36
Identities = 57/208 (27%), Positives = 97/208 (46%), Gaps = 27/208 (12%)
Query: 73 KRSLRSKIRKDLKNMDPIQRSQEDTAVQDIVLESSWFKASRNICAYISCASLREVDTSRI 132
K+ LR ++ + + +R+ A+ + + ++ + Y+S E+DT +
Sbjct: 1 KQELRKQLLAKRRALSEEERAAASRALHQKLPSFVGAQKAKRVALYVSVK--GEIDTREL 58
Query: 133 VSEILSNQTDGNGQMRKKLYVPRVEDKNSNMRMLKISAVKD-LVANSMNILEPSLLDSDG 191
+ +L + K + +PR + + + + L + + EP +
Sbjct: 59 IELLL--------EEGKLVLLPRPRPDSGLVVRITPYYPETGLPSGPYGLPEPI----EE 106
Query: 192 NQCEDVMQASEPVDLLILPGLAFDRSGGRLGRGGGYYDVFLKKYQKLAQEQKWKQPLLVA 251
Q E A +DL+++PG+AFDR G RLGRGGGYYD +L + Q PL V
Sbjct: 107 EQREL---ALNQIDLVLVPGVAFDRQGYRLGRGGGYYDRYLARLQ-------GHGPLTVG 156
Query: 252 LLYSLQLVDEESIPVTPYDVPVDALVSP 279
L Y QLV+ +P P+DVPVD +V+
Sbjct: 157 LAYDEQLVER--LPQEPHDVPVDEIVTE 182
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 126 bits (318), Expect = 1e-35
Identities = 57/211 (27%), Positives = 97/211 (45%), Gaps = 27/211 (12%)
Query: 73 KRSLRSKIRKDLKNMDPIQRSQEDTAVQDIVLESSWFKASRNICAYISCASLREVDTSRI 132
K +LR + + + P +R + D + ++ K ++ I Y+ E+DT +
Sbjct: 5 KSALRKLLLERRIALSPEERHEADQRIAKLLASLIEVKKAKTIALYVPFNG--EIDTRPL 62
Query: 133 VSEILSNQTDGNGQMRKKLYVPRVEDKNSNMRMLKISAVKDLVANSMNILEPSLLDSDGN 192
+ + L G K+L +P++ D ++ L+ N ILEP
Sbjct: 63 IRQALR---RG-----KRLLLPKLRDYKLLFLRYIPDPLQPLIKNRFGILEP-----GEY 109
Query: 193 QCEDVMQASEPVDLLILPGLAFDRSGGRLGRGGGYYDVFLKKYQKLAQEQKWKQPLLVAL 252
+ +DL+++P +AFD+ G RLG GGGYYD +L + ++ V +
Sbjct: 110 GRK---IPPPEIDLVLVPLVAFDKQGYRLGYGGGYYDRYLANLR-------GRKTPTVGI 159
Query: 253 LYSLQLVDEESIPVTPYDVPVDALVSPRGFI 283
Y QLVD +P P+DVP+DA+V+ G I
Sbjct: 160 AYDCQLVDH--LPREPHDVPLDAIVTEEGVI 188
>gnl|CDD|182385 PRK10333, PRK10333, 5-formyltetrahydrofolate cyclo-ligase family
protein; Provisional.
Length = 182
Score = 69.2 bits (169), Expect = 3e-14
Identities = 46/132 (34%), Positives = 68/132 (51%), Gaps = 17/132 (12%)
Query: 149 KKLYVPRVED-KNSNMRMLKISAVKDLVANSMNILEPSLLDSDGNQCEDVMQASEPVDLL 207
K++Y+P + N+ L +LV N + I EP L DV+ S +D+L
Sbjct: 61 KRVYLPVLHPFSAGNLLFLNYHPQSELVMNRLKIHEPKL------DVRDVLPLSR-LDVL 113
Query: 208 ILPGLAFDRSGGRLGRGGGYYDVFLKKYQKLAQEQKWKQPLLVALLYSLQLVDEESIPVT 267
I P +AFD G RLG GGG+YD L+ +Q QP V + QLV+ +PV
Sbjct: 114 ITPLVAFDEYGQRLGMGGGFYDRTLQNWQ-----HYKTQP--VGYAHDCQLVE--KLPVE 164
Query: 268 PYDVPVDALVSP 279
+D+P+ A+V+P
Sbjct: 165 EWDIPLPAVVTP 176
>gnl|CDD|224165 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 358
Score = 30.1 bits (68), Expect = 1.4
Identities = 11/92 (11%), Positives = 33/92 (35%), Gaps = 11/92 (11%)
Query: 56 MNNNVVDPHQLEAIFQKKRSLRSKIRKD-----LKNMDPIQRSQEDTAVQDIVLES---S 107
+ N + H+ + + R R + D D ++ + ++L +
Sbjct: 1 SDKNKIMAHRELVLKIRMRKKRKRGDPDKPVAVWIEEDRLRGYPGKSLT--VILRTRGCR 58
Query: 108 WFKASR-NICAYISCASLREVDTSRIVSEILS 138
W++ +C Y + ++ V ++++
Sbjct: 59 WYREGGCYMCGYPADSAGEPVSEENLINQFDE 90
>gnl|CDD|236010 PRK07395, PRK07395, L-aspartate oxidase; Provisional.
Length = 553
Score = 30.0 bits (68), Expect = 1.4
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 197 VMQASEPVDLLILPGLAFDRSGGRL 221
V QA E + L+ G+AFDR G L
Sbjct: 88 VEQAPEAIASLVEMGVAFDRHGQHL 112
>gnl|CDD|224235 COG1316, LytR, Transcriptional regulator [Transcription].
Length = 307
Score = 29.7 bits (67), Expect = 1.5
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 23 ARLIRNAKEIAPVTHLPTTPLSAVSSNVRTNIVMNNNVVD 62
L + + L+ +SSN +TNI +NN
Sbjct: 207 TALANKMLSPNSIFKYQSL-LNDISSNFKTNITINNLTAL 245
>gnl|CDD|215004 smart01061, CAT_RBD, CAT RNA binding domain. This RNA binding
domain is found at the amino terminus of
transcriptional antitermination proteins such as BglG,
SacY and LicT. These proteins control the expression of
sugar metabolising operons in Gram+ and Gram- bacteria.
This domain has been called the CAT (Co-AntiTerminator)
domain. It binds as a dimer.to short Ribonucleotidic
Anti-Terminator (RAT) hairpin, each monomer interacting
symmetrically with both strands of the RAT hairpin. In
the full-length protein, CAT is followed by two
phosphorylatable PTS regulation domains that modulate
the RNA binding activity of CAT. Upon activation, the
dimeric proteins bind to RAT targets in the nascent
mRNA, thereby preventing abortive dissociation of the
RNA polymerase from the DNA template.
Length = 55
Score = 27.1 bits (61), Expect = 1.7
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 10/29 (34%)
Query: 55 VMNNNVV---DPHQLEAI-------FQKK 73
V+NNNVV D + E I F KK
Sbjct: 6 VLNNNVVLAEDENGQEVIVMGKGIGFGKK 34
>gnl|CDD|114305 pfam05575, V_cholerae_RfbT, Vibrio cholerae RfbT protein. This
family consists of several RfbT proteins from Vibrio
cholerae. It has been found that genetic alteration of
the rfbT gene is responsible for serotype conversion of
Vibrio cholerae O1 and determines the difference between
the Ogawa and Inaba serotypes, in that the presence of
rfbT is sufficient for Inaba-to-Ogawa serotype
conversion.
Length = 286
Score = 28.9 bits (64), Expect = 3.4
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 12 GQSMFRHCKTTARLIRNAKEIAPVTHLPTTPLSAVSSNVRTNIVMNNNVVDPHQL 66
G ++ C AR I K IA PL+ + +++R N+ +NN +V+ H
Sbjct: 87 GANVGTFCGIAARHITQGKIIA------IEPLTEMENSIRMNVQLNNPLVEFHHF 135
>gnl|CDD|131814 TIGR02767, TraG-Ti, Ti-type conjugative transfer system protein
TraG. This protein is found in the Agrobacterium
tumefaciens Ti plasmid tra region responsible for
conjugative transfer of the entire plasmid among
Agrobacterium strains. The protein is distantly related
to the F-type conjugation system TraG protein. Both of
these systems are examples of type IV secretion systems.
Length = 623
Score = 28.3 bits (63), Expect = 5.6
Identities = 11/30 (36%), Positives = 23/30 (76%), Gaps = 4/30 (13%)
Query: 106 SSWFKASRNICAYISCASLREVDTSRIVSE 135
SSWF++ C++IS A+++++DT+ +S+
Sbjct: 517 SSWFES----CSFISYAAIKDLDTADYISK 542
>gnl|CDD|226494 COG4006, COG4006, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 278
Score = 27.5 bits (61), Expect = 8.3
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 11/78 (14%)
Query: 81 RKDLKNMDPIQRSQEDTAVQDIVLESSW-----------FKASRNICAYISCASLREVDT 129
R L + D + E+ + W F+AS + A ++
Sbjct: 21 RLGLPDADRARMDDEECGRRLSRGSELWKVLEKLVSYAPFRASAELNTLFISAERKDRSV 80
Query: 130 SRIVSEILSNQTDGNGQM 147
S I IL + NG++
Sbjct: 81 SEIDEAILYSTDTANGRL 98
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.132 0.375
Gapped
Lambda K H
0.267 0.0851 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,633,107
Number of extensions: 1364175
Number of successful extensions: 1177
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1165
Number of HSP's successfully gapped: 16
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.3 bits)