Align cobalamin-independent methionine synthase (EC 2.1.1.14) (characterized)
to candidate WP_005459760.1 SACCYDRAFT_RS22695 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= metacyc::G18NG-10711-MONOMER
(745 letters)
>NCBI__GCF_000244975.1:WP_005459760.1
Length = 762
Score = 726 bits (1875), Expect = 0.0
Identities = 410/769 (53%), Positives = 503/769 (65%), Gaps = 34/769 (4%)
Query: 1 MTSNFSSTVAGLPRIGAKRELKFALEGYWNGSIEGRELAQTARQLVNTASDSL--SGLDS 58
MTS STV G PRIG RELK ALE YW I EL AR L SL +GLDS
Sbjct: 1 MTSTIGSTVLGYPRIGPNRELKRALENYWASRISEAELRNIARDLRIDTWRSLRQAGLDS 60
Query: 59 VPFAGRSYYDAMLDTAAILGVLPERFDDIADHENDGLPLWIDRYFGAARGTETLPAQAMT 118
VP S+YD +LDTA G +P R+ D+ GL +D YF ARG E+ P +T
Sbjct: 61 VPGNTFSFYDHVLDTAVTFGAVPRRYADL------GLSP-LDTYFAMARGVESTPPLELT 113
Query: 119 KWFDTNYHYLVPELSADTRFVLDASALIEDLRCQQVRGVNARPVLVGPLTFLSLAR---- 174
KWFDTNYHYLVPE+ DTRF L ++E +R G+ RPVLVGP+TFL L++
Sbjct: 114 KWFDTNYHYLVPEIGPDTRFFLADHGVLEQVREADELGIPVRPVLVGPVTFLLLSKPDSE 173
Query: 175 TTDGSNPLDHLPALFEVYERLIKSF---DTEWVQIDEPALVTDVAPEVLEQVRAGYTTL- 230
G PLD + L + Y L++ EWVQ+DEPA D L +R Y +L
Sbjct: 174 AAPGFRPLDTVDELVDAYAELLRELARAGVEWVQLDEPAFAADRTEAELAALREAYRSLG 233
Query: 231 --AKRDGVFVNTYFGSGDQALNTLAGIGLGAIGVDLVTH--GVTELAAWKG--EELLVAG 284
A+R +FV YFG +AL L+ + A+GVD V G+ LAA G ++ LVAG
Sbjct: 234 SLAERPKLFVAGYFGDLGEALEILSAAPVEAVGVDFVAGDPGLDSLAALPGLRDKTLVAG 293
Query: 285 IVDGRNIWRTDLCAALASLKRLAA-RGPIAVSTSCSLLHVPYTLEAEN-IEPEVRDWLAF 342
+VDGRN+WRTDL AL + L G +AVS+SCSLLHVPY +EAE+ ++P+V WLAF
Sbjct: 294 LVDGRNVWRTDLDRALTTAATLLGLAGEVAVSSSCSLLHVPYDVEAESSLDPQVASWLAF 353
Query: 343 GSEKITEVKLLADALAGNIDAAAFDAASAA-IASRRTSP---RTAPITQELPG-----RS 393
+K+ EV +L AL DA A + A+A + + R + R + + L G
Sbjct: 354 ARQKVHEVVVLGRALREGRDAVAEELAAARRVVTDRVNAERVRDEQVRRRLAGLRPRDTR 413
Query: 394 RGSFDTRVTLQEKSLELPALPTTTIGSFPQTPSIRSARARLRKESITLEQYEEAMREEID 453
R +D R Q+++L LP LPTTTIGSFPQT +R RA LR+ I + Y MR EI+
Sbjct: 414 RADYDVRREAQQEALRLPPLPTTTIGSFPQTADVRRTRAALRRGGIDHDTYISRMRAEIE 473
Query: 454 LVIAKQEELGLDVLVHGEPERNDMVQYFSELLDGFLSTANGWVQSYGSRCVRPPVLFGNV 513
V+ QEELGLDVLVHGEPERNDMVQYF+E L GF T +GWVQSYGSRCVRPP+LFG+V
Sbjct: 474 RVVRLQEELGLDVLVHGEPERNDMVQYFAEHLAGFADTEHGWVQSYGSRCVRPPILFGDV 533
Query: 514 SRPAPMTVKWFQYAQSLTQKHVKGMLTGPVTILAWSFVRDDQPLATTADQVALALRDEIN 573
SRP P+TV+W YA SLT + VKGMLTGPVTILAWSFVRDDQPLA TA QVALA+RDEI
Sbjct: 534 SRPEPITVEWAAYAASLTDRPVKGMLTGPVTILAWSFVRDDQPLADTAKQVALAIRDEIA 593
Query: 574 DLIEAGAKIIQVDEPAIRELLPLRDVDKPAYLQWSVDSFRLATAGAPDDVQIHTHMCYSE 633
DL AG +IQVDEPA+RELLPLR YL W+V++FRLAT+GA Q+HTH+CYSE
Sbjct: 594 DLEAAGLGVIQVDEPALRELLPLRAHRHKEYLDWAVEAFRLATSGARASTQVHTHLCYSE 653
Query: 634 FNEVISSVIALDADVTTIEAARSDMQVLAALKSSGFELGVGPGVWDIHSPRVPSAQEVDG 693
F +VI ++ ALDADVT+IEAARS M+VL L ++GF GVGPGV+DIHSPRVP E
Sbjct: 654 FGDVIDAIAALDADVTSIEAARSRMEVLGDLGAAGFARGVGPGVYDIHSPRVPEVAETVE 713
Query: 694 LLEAALQSVDPRQLWVNPDCGLKTRGWPEVEASLKVLVESAKQAREKIG 742
LL AAL SV P +LWVNPDCGLKTRG+ EVE +L+ LV +A + R +G
Sbjct: 714 LLRAALASVPPSRLWVNPDCGLKTRGYAEVEPALRNLVAAATEVRRTLG 762
Lambda K H
0.317 0.134 0.392
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1470
Number of extensions: 61
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 745
Length of database: 762
Length adjustment: 40
Effective length of query: 705
Effective length of database: 722
Effective search space: 509010
Effective search space used: 509010
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: 55 (25.8 bits)
Align candidate WP_005459760.1 SACCYDRAFT_RS22695 (5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase)
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.aa/TIGR01371.hmm
# target sequence database: /tmp/gapView.8391.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01371 [M=754]
Accession: TIGR01371
Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1044.8 0.0 0 1044.6 0.0 1.0 1 lcl|NCBI__GCF_000244975.1:WP_005459760.1 SACCYDRAFT_RS22695 5-methyltetra
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005459760.1 SACCYDRAFT_RS22695 5-methyltetrahydropteroyltriglutamate--homocysteine S-me
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1044.6 0.0 0 0 1 753 [. 10 759 .. 10 760 .. 0.98
Alignments for each domain:
== domain 1 score: 1044.6 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lg+Prig++Relk+ale+yw+ +is++el + a+dlr ++++++++ag+d++p n+fs+YDhvLdtav
lcl|NCBI__GCF_000244975.1:WP_005459760.1 10 LGYPRIGPNRELKRALENYWASRISEAELRNIARDLRIDTWRSLRQAGLDSVPGNTFSFYDHVLDTAVT 78
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknkllee 138
+ga+p+r+ +l + s ldtyFa+aRG e+ ++ le+tkwf+tnYhYlvPe+ ++++f l+ + +le+
lcl|NCBI__GCF_000244975.1:WP_005459760.1 79 FGAVPRRYADL--GLSPLDTYFAMARGVES--TPPLELTKWFDTNYHYLVPEIGPDTRFFLADHGVLEQ 143
**********9..5557**********966..89*********************************** PP
TIGR01371 139 ykeakelgvetkPvllGpitflkLakakee..eekellellekllpvYkevlkklaeagvewvqidePv 205
++ea elg+ ++Pvl+Gp+tfl+L+k ++e +++l+++++l+++Y e+l++la agvewvq+deP+
lcl|NCBI__GCF_000244975.1:WP_005459760.1 144 VREADELGIPVRPVLVGPVTFLLLSKPDSEaaPGFRPLDTVDELVDAYAELLRELARAGVEWVQLDEPA 212
**************************9988666899********************************* PP
TIGR01371 206 lvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee.lelak 273
++ d +++elaa++eay++l + +++ kl+++ Yf+++ eale l+ pvea+g+D+v+++ +la+
lcl|NCBI__GCF_000244975.1:WP_005459760.1 213 FAADRTEAELAALREAYRSLGSLAERPKLFVAGYFGDLGEALEILSAAPVEAVGVDFVAGDPGlDSLAA 281
***********************************************************9987678899 PP
TIGR01371 274 akfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelke 342
+dk+LvaG++dGrn+w++dl ++l++ ++l a +++vs+scsllhvp+d+e+e++ld+++ +
lcl|NCBI__GCF_000244975.1:WP_005459760.1 282 LPGLRDKTLVAGLVDGRNVWRTDLDRALTTAATLLGLA-GEVAVSSSCSLLHVPYDVEAESSLDPQVAS 349
9999*******************************999.56**************************** PP
TIGR01371 343 llafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressf 410
+lafa++k++e+ vl +al++ ++avae+l+a+++ ++ r + +rv de+v++rl+ l+ + +r++++
lcl|NCBI__GCF_000244975.1:WP_005459760.1 350 WLAFARQKVHEVVVLGRALREgRDAVAEELAAARRVVTDRVNAERVRDEQVRRRLAGLRPR-DTRRADY 417
********************99************************************997.778899* PP
TIGR01371 411 eeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDv 479
+ R+eaq++ l+lP lPtttiGsfPqt++vR++Ra++r+g i++++Y + +++ei++v++lqeelglDv
lcl|NCBI__GCF_000244975.1:WP_005459760.1 418 DVRREAQQEALRLPPLPTTTIGSFPQTADVRRTRAALRRGGIDHDTYISRMRAEIERVVRLQEELGLDV 486
********************************************************************* PP
TIGR01371 480 LvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpv 548
LvhGe+eRnDmv+yF+e+laGfa t++gWvqsYGsRcv+Ppi++gdvsrp+p+tv++ +ya slt++pv
lcl|NCBI__GCF_000244975.1:WP_005459760.1 487 LVHGEPERNDMVQYFAEHLAGFADTEHGWVQSYGSRCVRPPILFGDVSRPEPITVEWAAYAASLTDRPV 555
********************************************************************* PP
TIGR01371 549 kGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeY 617
kGmLtGPvtil+WsfvR+D+p++++a+q+ala+rde++dLe+ag+ +iq+DepalRe lPlr++ ++eY
lcl|NCBI__GCF_000244975.1:WP_005459760.1 556 KGMLTGPVTILAWSFVRDDQPLADTAKQVALAIRDEIADLEAAGLGVIQVDEPALRELLPLRAHRHKEY 624
********************************************************************* PP
TIGR01371 618 ldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyeke 686
ldwaveaFrla+sg++++tq+hth+CYsef ++i+aiaaldaDv+siea+rs me+l +l + +++++
lcl|NCBI__GCF_000244975.1:WP_005459760.1 625 LDWAVEAFRLATSGARASTQVHTHLCYSEFGDVIDAIAALDADVTSIEAARSRMEVLGDLGA-AGFARG 692
*************************************************************9.88**** PP
TIGR01371 687 iGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
+G+GvyDihsprvP + e ell++al+++p +rlWvnPDCGLktR + ev++al+nlv+aa e+R
lcl|NCBI__GCF_000244975.1:WP_005459760.1 693 VGPGVYDIHSPRVPEVAETVELLRAALASVPPSRLWVNPDCGLKTRGYAEVEPALRNLVAAATEVRR 759
****************************************************************996 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (762 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 8.38
//
[ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory