Align 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 2; Cobalamin-independent methionine synthase 2; AtMS2; EC 2.1.1.14 (characterized)
to candidate WP_013554048.1 NITSA_RS05615 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= SwissProt::Q9SRV5
(765 letters)
>NCBI__GCF_000186245.1:WP_013554048.1
Length = 767
Score = 688 bits (1776), Expect = 0.0
Identities = 381/766 (49%), Positives = 496/766 (64%), Gaps = 17/766 (2%)
Query: 6 VGYPRMGPKRELKFALESFWDGKSSADDLQKVSADLRSDIWKQMSAAGIKYIPSNTFSHY 65
+G+ R+G KRELKFALE +W +SS ++L+K SA LR W A GI I N FS Y
Sbjct: 9 IGFGRIGEKRELKFALEKYWKKESSLEELEKTSAQLRRRHWDYQCAVGIDAISCNDFSWY 68
Query: 66 DQVLDTTAMLGAVPSRYGFTSGEIGLDVYFSMARGNASVPAMEMTKWFDTNYHYIVPELG 125
DQ LD LG P R+ S + + YF+MARG+ S PAMEMTKWF+TNYHYIVPEL
Sbjct: 69 DQTLDMIVALGLEPERFRTISDPV--ERYFAMARGDESRPAMEMTKWFNTNYHYIVPELS 126
Query: 126 PEVKFSYASHKAVNEYKEAKALGVETVPV-LVGPVSYLLLSKLAKGVDKSFDLLSLLPKI 184
++ + + Y EAKA G+E + L+GP+++L +K D D L L +I
Sbjct: 127 AALQGRADASGIIARYAEAKAQGIEHPKINLIGPLTFLANAKRPDSPD--VDALGLFDRI 184
Query: 185 LPVYKEVIAELKAAGASWI--QLDEPLFVMDLEGHKLQAFSGAYAELESTLSGLNVLVET 242
LP+Y+ ++ +L I Q++EP+FV D AY L S S L + V +
Sbjct: 185 LPLYETLLTQLAQLDEEEIIIQMEEPVFVTDKAAQMGLLIRNAYERLASIDSRLKLYVVS 244
Query: 243 YFADIPAEAYKTLTSLKGVTAFGFDLVRGT-KTIDLIKSGFPQGKYLFAGVVDGRNIWAN 301
YF D EA + L V G D + + + +++ GK L AGV+DGRNIW
Sbjct: 245 YF-DHAVEAARVLAQTP-VAGIGLDFLYDEGQNREALQAIADSGKTLIAGVIDGRNIWRT 302
Query: 302 DLAASLITLQSLEGVVGKDKLVVSTSCSLLHTAVDLINETKLDAEIKSWLAFAAQKVVEV 361
DL L L+S+ V +++++S SCSLLH L E K+D +KS+LAFA +++ E+
Sbjct: 303 DLDKRLELLESIAQTVPAERVILSPSCSLLHIPFTLRYEEKMDPAVKSYLAFATERLEEL 362
Query: 362 DAL-----AKALAGQTNESFFTANADALSSRRSSPRVTNESVQKAAAALKGSDHRRTTEV 416
+ L K+LA ++ + AL+ RR S VT+ +VQ+ AL +R T
Sbjct: 363 NVLNALFRKKSLA-ESQHQVLEESRCALAKRRESSHVTDPAVQERMKALDTLRRKRKTPF 421
Query: 417 SARLDAQQKKLNLPILPTTTIGSFPQTVELRRVRREYKAKKISEEDYVKAIKEEIKKVVD 476
R+ Q ++ L TTTIGSFPQT ELR++RR+YK +I E Y + I+E+IK V+
Sbjct: 422 KERIVTQHRRFGYKPLATTTIGSFPQTPELRKMRRDYKEGRIDAETYERYIEEQIKACVE 481
Query: 477 IQEDLDIDVLVHGEPERNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPVIYGDVSRPK 536
QE +D+++LVHGE ERNDMVEYFGEQLSG AF+ NGWVQSYGSRCVKPP+IYGDVSRP
Sbjct: 482 FQERIDLEILVHGEFERNDMVEYFGEQLSGVAFSENGWVQSYGSRCVKPPLIYGDVSRPA 541
Query: 537 PMTVFWSSTAQSMTKRPMKGMLTGPVTILNWSFVRNDQPRHETCYQIALAIKDEVEDLEK 596
PMTV WS+ AQS+T+RPMKGMLTGPVTILNWSFVR+DQPR ETCYQIALAI+DEV+DL+K
Sbjct: 542 PMTVRWSTFAQSLTERPMKGMLTGPVTILNWSFVRDDQPRSETCYQIALAIRDEVDDLQK 601
Query: 597 GGIGVIQIDEAALREGLPLRKAEHSFYLDWAVHSFRITNCGVQDSTQIHTHMCYSNFNDI 656
GIG+IQ+DEAA +EG PLR A+ Y +A+ SF I + TQIHTHMCYS FNDI
Sbjct: 602 AGIGMIQVDEAAFKEGYPLRSAKRPEYERFALESFWIATNVAEPETQIHTHMCYSEFNDI 661
Query: 657 IHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTDEIADRIN 716
I +I MDADVI+IE +RS LL +F+E Y IGPGVYDIHSPR+PS DE+ D+I+
Sbjct: 662 IDTIEGMDADVISIETARSGNVLLRIFKER-GYEMEIGPGVYDIHSPRVPSVDEMVDQIH 720
Query: 717 KMLAVLEQNILWVNPDCGLKTRKYTEVKPALKAMVDAAKLIRSQLG 762
+L VL LW+NPDCGLKTR + EV+ +L MV A K +R +LG
Sbjct: 721 ALLEVLPPRQLWINPDCGLKTRGWPEVEASLANMVQAVKEVRQELG 766
Lambda K H
0.317 0.133 0.385
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: 1309
Number of extensions: 49
Number of successful extensions: 8
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: 765
Length of database: 767
Length adjustment: 41
Effective length of query: 724
Effective length of database: 726
Effective search space: 525624
Effective search space used: 525624
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_013554048.1 NITSA_RS05615 (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.6912.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.1e-302 990.7 0.0 4.7e-302 990.5 0.0 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013554048.1 NITSA_RS05615 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000186245.1:WP_013554048.1 NITSA_RS05615 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 990.5 0.0 4.7e-302 4.7e-302 1 754 [] 9 764 .. 9 764 .. 0.97
Alignments for each domain:
== domain 1 score: 990.5 bits; conditional E-value: 4.7e-302
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
+gf rigekRelk+alekywk+++s eel+k++++lr+++++ q + g+d i+ ndfs+YD+ Ld+ v
lcl|NCBI__GCF_000186245.1:WP_013554048.1 9 IGFGRIGEKRELKFALEKYWKKESSLEELEKTSAQLRRRHWDYQCAVGIDAISCNDFSWYDQTLDMIVA 77
69******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknkllee 138
lg perf++++d +++yFa+aRG+e+ +a+emtkwfntnYhY+vPels++ + + +++ ++ +
lcl|NCBI__GCF_000186245.1:WP_013554048.1 78 LGLEPERFRTISD---PVERYFAMARGDES--RPAMEMTKWFNTNYHYIVPELSAALQGRADASGIIAR 141
**********933...479********966..89*********************************** PP
TIGR01371 139 ykeakelgvet.kPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvew..vqideP 204
y eak++g+e k l+Gp+tfl ak+ ++ + ++l l +++lp+Y+ +l++la+ + e+ +q++eP
lcl|NCBI__GCF_000186245.1:WP_013554048.1 142 YAEAKAQGIEHpKINLIGPLTFLANAKRPDSPDVDALGLFDRILPLYETLLTQLAQLDEEEiiIQMEEP 210
********87526679*************9999*********************987766522799*** PP
TIGR01371 205 vlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee.lela 272
v+v+d +++ ++++aye l++ ++lkl++ +Yfd+ ea + l+++pv+++glD+ ++ + e+
lcl|NCBI__GCF_000186245.1:WP_013554048.1 211 VFVTDKAAQMGLLIRNAYERLASIDSRLKLYVVSYFDHAVEAARVLAQTPVAGIGLDFLYDEGQnREAL 279
***********************************************************9999856667 PP
TIGR01371 273 kakfeedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvpvdleleekldkel 340
+a ++ k+L+aGvidGrniw++dl k l+ll+++++++ +++++s+scsllh+p++l+ eek+d+++
lcl|NCBI__GCF_000186245.1:WP_013554048.1 280 QAIADSGKTLIAGVIDGRNIWRTDLDKRLELLESIAQTVPaERVILSPSCSLLHIPFTLRYEEKMDPAV 348
7778899*****************************99988**************************** PP
TIGR01371 341 kellafakekleelkvlkealeg...eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarr 406
k++lafa+e+leel+vl+ ++++ +++++ le+++ a+a+r++s+ v+d +v+er++al++ + +r
lcl|NCBI__GCF_000186245.1:WP_013554048.1 349 KSYLAFATERLEELNVLNALFRKkslAESQHQVLEESRCALAKRRESSHVTDPAVQERMKALDTLRRKR 417
*******************99874344567778999999****************************** PP
TIGR01371 407 essfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeel 475
+++f+eR +q++++ l tttiGsfPqt e+Rk+R+++++g+i++e+Ye+ i+e+ik ++++qe++
lcl|NCBI__GCF_000186245.1:WP_013554048.1 418 KTPFKERIVTQHRRFGYKPLATTTIGSFPQTPELRKMRRDYKEGRIDAETYERYIEEQIKACVEFQERI 486
********************************************************************* PP
TIGR01371 476 glDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqslt 544
+l++LvhGefeRnDmveyFge+l+G af +ngWvqsYGsRcvkPp+iygdvsrp+pmtv++s++aqslt
lcl|NCBI__GCF_000186245.1:WP_013554048.1 487 DLEILVHGEFERNDMVEYFGEQLSGVAFSENGWVQSYGSRCVKPPLIYGDVSRPAPMTVRWSTFAQSLT 555
********************************************************************* PP
TIGR01371 545 skpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksd 613
++p+kGmLtGPvtilnWsfvR+D+pr+e+++qiala+rdev dL++agi +iq+De+a++eg Plr+++
lcl|NCBI__GCF_000186245.1:WP_013554048.1 556 ERPMKGMLTGPVTILNWSFVRDDQPRSETCYQIALAIRDEVDDLQKAGIGMIQVDEAAFKEGYPLRSAK 624
********************************************************************* PP
TIGR01371 614 keeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikk 682
+ eY ++a+e+F +a++ +++etqihthmCYsefn+ii++i+ +daDvisie++rs ll +ke ++
lcl|NCBI__GCF_000186245.1:WP_013554048.1 625 RPEYERFALESFWIATNVAEPETQIHTHMCYSEFNDIIDTIEGMDADVISIETARSGNVLLRIFKE-RG 692
******************************************************************.89 PP
TIGR01371 683 yekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakel 751
ye eiG+GvyDihsprvPs++e+ +++++ l++lp ++lW+nPDCGLktR w+ev+a+l n+v+a+ke+
lcl|NCBI__GCF_000186245.1:WP_013554048.1 693 YEMEIGPGVYDIHSPRVPSVDEMVDQIHALLEVLPPRQLWINPDCGLKTRGWPEVEASLANMVQAVKEV 761
********************************************************************* PP
TIGR01371 752 Rek 754
R++
lcl|NCBI__GCF_000186245.1:WP_013554048.1 762 RQE 764
*85 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (767 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 10.91
//
[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