Align cobalamin-independent methionine synthase (EC 2.1.1.14) (characterized)
to candidate WP_058932241.1 AU252_RS20200 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= metacyc::G18NG-10711-MONOMER
(745 letters)
>NCBI__GCF_001484605.1:WP_058932241.1
Length = 779
Score = 704 bits (1818), Expect = 0.0
Identities = 398/762 (52%), Positives = 490/762 (64%), Gaps = 32/762 (4%)
Query: 6 SSTVAGLPRIGAKRELKFALEGYWNGSIEGRELAQTARQLVNTASDSLSGLDSVPFAGR- 64
++++ G PR+G +RELK A+E YW G I+ L A+ + T + L L A
Sbjct: 13 AASLLGYPRVGRRRELKKAIEAYWAGKIDADALDAAAKGIQLTIAKRLQELGLTEAAAVP 72
Query: 65 ---SYYDAMLDTAAILGVLPERFDDIADHENDGLPLWIDRYFGAARGTETLPAQAMTKWF 121
SYYD +LD A LG +P RF + + E L ID YF ARGT+ MTKWF
Sbjct: 73 GTFSYYDQVLDATAHLGAVPARFGKLLNAEGQ---LDIDGYFTLARGTKDQQPLEMTKWF 129
Query: 122 DTNYHYLVPELSADTRFVLDASALIEDLRCQQVRGVNARPVLVGPLTFLSLARTTD---- 177
DTNYHYLVPE+ +T F L ++ ++E+ G+ RP +VGP+T+L L++ +D
Sbjct: 130 DTNYHYLVPEIGPETEFTLASNRIVEEFEFALANGIETRPYIVGPVTYLLLSKASDEAPA 189
Query: 178 GSNPLDHLPALFEVYERLIKSF---DTEWVQIDEPALVTDV---APEVLEQVRAGYTTL- 230
G PL L + VY +L++ W+Q+DEPALV D A E+ V Y L
Sbjct: 190 GFAPLSRLEDVLPVYVQLLEKLAAAGASWIQLDEPALVVDQDTPAAEIEAAVARAYEVLS 249
Query: 231 --AKRDGVFVNTYFGSGDQALNTLAGIGLGAIGVDLVTHGVTELAAWKG--EELLVAGIV 286
AKR + V+T +G+ D L TLA + A+ +D V AA G + LVAG+V
Sbjct: 250 GAAKRPQILVSTPYGALDGQLGTLAATNIDALHIDAFKGAVPSAAALAGLGNKTLVAGVV 309
Query: 287 DGRNIWRTDLCAALASLKRL-AARGPIAVSTSCSLLHVPYTLEAEN-IEPEVRDWLAFGS 344
DG NIWR DL A A L L AA G IAVSTS S HVP+ + E + E+R WLAF
Sbjct: 310 DGHNIWRNDLAVAAAKLDELKAAAGRIAVSTSTSTQHVPHDVTEEGQLSEELRSWLAFAD 369
Query: 345 EKITEVKLLADALAGNIDA-AAFDAASAAIASR-------RTSPRTAPITQELPGRSRGS 396
+K EVK LA LA A AA D ASA IA+R R R +R +
Sbjct: 370 QKAVEVKTLASYLADPASAKAAIDEASAVIAARAIAEGVRRDDVRARTEALTAADFNRSA 429
Query: 397 FDTRVTLQEKSLELPALPTTTIGSFPQTPSIRSARARLRKESITLEQYEEAMREEIDLVI 456
+ R QE++L LP LPTTTIGSFPQT IRSARAR K ++T EQYE+ M++EI V+
Sbjct: 430 YAVREAAQEEALHLPPLPTTTIGSFPQTSEIRSARARNNKGALTNEQYEQLMKDEIKRVV 489
Query: 457 AKQEELGLDVLVHGEPERNDMVQYFSELLDGFLSTANGWVQSYGSRCVRPPVLFGNVSRP 516
QEELG DVLVHGEPERNDMVQYF+E L+GF T +GWVQSYGSRC RP +L+G+V+R
Sbjct: 490 ELQEELGYDVLVHGEPERNDMVQYFAENLEGFDVTVHGWVQSYGSRCTRPSILWGDVTRS 549
Query: 517 APMTVKWFQYAQSLTQKHVKGMLTGPVTILAWSFVRDDQPLATTADQVALALRDEINDLI 576
AP+TV W +YAQSLT K +KGMLTGPVTILAWSFVRDDQPL TA+QV LALRDEI DL
Sbjct: 550 APITVAWAEYAQSLTSKPMKGMLTGPVTILAWSFVRDDQPLGETANQVGLALRDEIADLE 609
Query: 577 EAGAKIIQVDEPAIRELLPLRDVDKPAYLQWSVDSFRLATAGAPDDVQIHTHMCYSEFNE 636
AG K+IQVDEPA+RELLPLR D YL+WSVDSFRLATAGA D QIHTH+CYSEF
Sbjct: 610 AAGIKVIQVDEPALRELLPLRKADHATYLKWSVDSFRLATAGAADATQIHTHLCYSEFGV 669
Query: 637 VISSVIALDADVTTIEAARSDMQVLAALKSSGFELGVGPGVWDIHSPRVPSAQEVDGLLE 696
+I ++ LDADVT+IEAARS M+V+ L+S GF GVGPGV+DIHSPRVP EV LL
Sbjct: 670 IIDAIDGLDADVTSIEAARSRMEVVHDLESHGFGRGVGPGVYDIHSPRVPGEAEVTELLA 729
Query: 697 AALQSVDPRQLWVNPDCGLKTRGWPEVEASLKVLVESAKQAR 738
A++ V RQLWVNPDCGLKTRG+ E E SL+ LV++ K R
Sbjct: 730 TAVKHVPSRQLWVNPDCGLKTRGYAETEESLRNLVKATKTVR 771
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: 1393
Number of extensions: 49
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: 779
Length adjustment: 40
Effective length of query: 705
Effective length of database: 739
Effective search space: 520995
Effective search space used: 520995
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_058932241.1 AU252_RS20200 (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.28145.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.7e-303 993.8 0.0 5.4e-303 993.6 0.0 1.0 1 lcl|NCBI__GCF_001484605.1:WP_058932241.1 AU252_RS20200 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058932241.1 AU252_RS20200 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 993.6 0.0 5.4e-303 5.4e-303 1 753 [. 17 772 .. 17 773 .. 0.96
Alignments for each domain:
== domain 1 score: 993.6 bits; conditional E-value: 5.4e-303
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipv..ndfslYDhvLdta 67
lg+Pr+g++Relkka+e+yw+gki++++l++ ak ++ + k+++e g+ ++ ++fs+YD+vLd++
lcl|NCBI__GCF_001484605.1:WP_058932241.1 17 LGYPRVGRRRELKKAIEAYWAGKIDADALDAAAKGIQLTIAKRLQELGLTEAAAvpGTFSYYDQVLDAT 85
79********************************************998654432389*********** PP
TIGR01371 68 vllgaiperfkel..addesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknk 134
+ lga+p+rf +l a+++ d+d yF++aRGt kd + lemtkwf+tnYhYlvPe+ +e+ef+l++n+
lcl|NCBI__GCF_001484605.1:WP_058932241.1 86 AHLGAVPARFGKLlnAEGQLDIDGYFTLARGT--KDQQPLEMTKWFDTNYHYLVPEIGPETEFTLASNR 152
***********972234567899********9..6799******************************* PP
TIGR01371 135 lleeykeakelgvetkPvllGpitflkLakakee..eekellellekllpvYkevlkklaeagvewvqi 201
++ee++ a ++g+et+P ++Gp+t+l+L+ka++e +++l++le++lpvY ++l+kla+ag++w+q+
lcl|NCBI__GCF_001484605.1:WP_058932241.1 153 IVEEFEFALANGIETRPYIVGPVTYLLLSKASDEapAGFAPLSRLEDVLPVYVQLLEKLAAAGASWIQL 221
********************************99788899***************************** PP
TIGR01371 202 dePvlvldlsk...eelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveake 267
deP+lv+d ++ e +aav +aye l+ a+k+ ++l++t +++++ +l +l+ ++++al++D +++
lcl|NCBI__GCF_001484605.1:WP_058932241.1 222 DEPALVVDQDTpaaEIEAAVARAYEVLSGAAKRPQILVSTPYGALDGQLGTLAATNIDALHIDAFKGAV 290
*******98641115567899***********************************************8 PP
TIGR01371 268 elelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekl 336
++a a++ +k+LvaGv+dG+niw++dl+ ++++l++l+a+a +++vsts+s+ hvp d+++e +l
lcl|NCBI__GCF_001484605.1:WP_058932241.1 291 PSAAALAGL-GNKTLVAGVVDGHNIWRNDLAVAAAKLDELKAAA-GRIAVSTSTSTQHVPHDVTEEGQL 357
866666655.569****************************999.78********************** PP
TIGR01371 337 dkelkellafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkar 405
++el+++lafa +k e+k+l++ l++ a++++a+++++a iaar+ + v ++v++r eal++++++
lcl|NCBI__GCF_001484605.1:WP_058932241.1 358 SEELRSWLAFADQKAVEVKTLASYLADPASAKAAIDEASAVIAARAIAEGVRRDDVRARTEALTAADFN 426
***************************9999*********************************99887 PP
TIGR01371 406 ressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqee 474
r s ++ R++aqe+ l+lP lPtttiGsfPqt+e+R+aRa+ +kg +++e+Ye+ +k+eik+v++lqee
lcl|NCBI__GCF_001484605.1:WP_058932241.1 427 R-SAYAVREAAQEEALHLPPLPTTTIGSFPQTSEIRSARARNNKGALTNEQYEQLMKDEIKRVVELQEE 494
6.579**************************************************************** PP
TIGR01371 475 lglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsl 543
lg DvLvhGe+eRnDmv+yF+e+l+Gf +t +gWvqsYGsRc +P+i++gdv+r +p+tv++ +yaqsl
lcl|NCBI__GCF_001484605.1:WP_058932241.1 495 LGYDVLVHGEPERNDMVQYFAENLEGFDVTVHGWVQSYGSRCTRPSILWGDVTRSAPITVAWAEYAQSL 563
********************************************************************* PP
TIGR01371 544 tskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrks 612
tskp+kGmLtGPvtil+WsfvR+D+p+ e+a+q++lalrde++dLe+agik+iq+DepalRe lPlrk+
lcl|NCBI__GCF_001484605.1:WP_058932241.1 564 TSKPMKGMLTGPVTILAWSFVRDDQPLGETANQVGLALRDEIADLEAAGIKVIQVDEPALRELLPLRKA 632
********************************************************************* PP
TIGR01371 613 dkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeik 681
d+++Yl+w+v++Frla++g++d+tqihth+CYsef ii+ai+ ldaDv+siea+rs me++++l++ +
lcl|NCBI__GCF_001484605.1:WP_058932241.1 633 DHATYLKWSVDSFRLATAGAADATQIHTHLCYSEFGVIIDAIDGLDADVTSIEAARSRMEVVHDLES-H 700
*******************************************************************.7 PP
TIGR01371 682 kyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaake 750
++ +++G+GvyDihsprvP + e++ell++a+k++p+++lWvnPDCGLktR + e++++l+nlv+a+k+
lcl|NCBI__GCF_001484605.1:WP_058932241.1 701 GFGRGVGPGVYDIHSPRVPGEAEVTELLATAVKHVPSRQLWVNPDCGLKTRGYAETEESLRNLVKATKT 769
8******************************************************************** PP
TIGR01371 751 lRe 753
+R+
lcl|NCBI__GCF_001484605.1:WP_058932241.1 770 VRA 772
*97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (779 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.63
//
[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