Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_012971451.1 ALVIN_RS11265 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000025485.1:WP_012971451.1
Length = 764
Score = 827 bits (2135), Expect = 0.0
Identities = 438/763 (57%), Positives = 529/763 (69%), Gaps = 20/763 (2%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
+ H LGFPR+G +RELK A ESYW G ST + L AVG ELRARHW Q QA +DL+PVGD
Sbjct: 3 ITHNLGFPRIGAKRELKFALESYWKGESTLDTLRAVGAELRARHW--QAQADLDLVPVGD 60
Query: 64 FAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGR-APTGEP-------AAAAEM 115
FA+YD +L S LG++P R G +DT FR+ RGR AP E AA EM
Sbjct: 61 FAFYDQMLDMSFTLGHLPKRVHGLKGE-SLDTYFRVARGRSAPAAEAQAGCTDGVAAGEM 119
Query: 116 TKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKG 175
TKWF+TNYHY+VPEF +FKL ++LL+++ EA G KPV++GPVT+L LGK K
Sbjct: 120 TKWFDTNYHYIVPEFTAATEFKLDASRLLEQLAEAKRQGVNAKPVIIGPVTYLALGKSK- 178
Query: 176 EQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-G 234
+ DRL+LL+ +LPVY ++L LA G++WVQIDEP LV EL + W A++ AY L+
Sbjct: 179 DGSDRLALLDRLLPVYAELLNTLAAHGVQWVQIDEPILVTELDETWRHAFEIAYHELKTA 238
Query: 235 QVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGR 294
VKLLL TYF + LPV GLH+D V G+DD+ L LPS +LS G+I+GR
Sbjct: 239 PVKLLLATYFGELQDQRYLAAHLPVAGLHIDAVRGRDDLVALLNLLPSSKILSLGVIDGR 298
Query: 295 NVWRADLT---EKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQ 351
N+W+ DL + I+D +G+R LW+A SCSLLH P+DL E LD E++SW AFA Q
Sbjct: 299 NIWKTDLNAVLDWLEPIQDQLGER-LWIAPSCSLLHVPVDLDSERTLDPEIRSWLAFARQ 357
Query: 352 KCHELALLRDALNSGDTAALAEWSA---PIQARRHSTRVHNPAVEKRLAAITAQDSQRAN 408
K +EL +L ALN G A AE A I +RR S RV++P V+ L I A+ +R +
Sbjct: 358 KLNELRVLATALNQGREAVRAELDANRAAIDSRRQSPRVNDPEVKASLTRIDARLGRRQS 417
Query: 409 VYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQA 468
Y RA Q LP +PTTTIGSFPQT EIR R FK G +D Y + I +
Sbjct: 418 PYADRAAKQAGLLNLPEFPTTTIGSFPQTGEIRQARRQFKAGTIDEATYVEIMRGEIARC 477
Query: 469 IVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISR 528
+ EQE LGLDVLVHGEAERNDMVEYFGE L GF F+Q GWVQSYGSRCVKPPI+ GDI R
Sbjct: 478 VREQEALGLDVLVHGEAERNDMVEYFGEQLAGFTFSQFGWVQSYGSRCVKPPILFGDIRR 537
Query: 529 PAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADL 588
P +TV+W YAQSLTDKP+KGMLTGPVTIL WSF R+D R +Q+ALA+R+EV DL
Sbjct: 538 PKAMTVDWITYAQSLTDKPMKGMLTGPVTILNWSFVRDDQPRSVSCRQLALAMREEVLDL 597
Query: 589 EAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFN 648
E AG+ +IQIDE ALREGLPLRRS W YL W VE FRI A D TQIHTHMCY EFN
Sbjct: 598 ERAGVRVIQIDEAALREGLPLRRSQWTDYLDWAVECFRITANGVSDATQIHTHMCYSEFN 657
Query: 649 DIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALL 708
DI+ SIA +DADVITIETSRSDMELL++F++F YPN IGPGVYDIHSPN+P + L+
Sbjct: 658 DIIASIADMDADVITIETSRSDMELLDAFDDFSYPNAIGPGVYDIHSPNIPGEAHMVELM 717
Query: 709 KKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
+KAA+RIPA+RLWVNPDCGLKTR W E AL NMV AA+ LR
Sbjct: 718 RKAAERIPAQRLWVNPDCGLKTRQWSEVIPALTNMVAAAKTLR 760
Lambda K H
0.319 0.135 0.416
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: 1669
Number of extensions: 78
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: 753
Length of database: 764
Length adjustment: 40
Effective length of query: 713
Effective length of database: 724
Effective search space: 516212
Effective search space used: 516212
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: 55 (25.8 bits)
Align candidate WP_012971451.1 ALVIN_RS11265 (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.20968.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 1109.8 0.0 0 1109.6 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012971451.1 ALVIN_RS11265 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012971451.1 ALVIN_RS11265 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1109.6 0.0 0 0 1 753 [. 7 761 .. 7 762 .. 0.99
Alignments for each domain:
== domain 1 score: 1109.6 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+kRelk+ale+ywkg+++ ++l +v ++lr++++++q+ ++d++pv+df++YD++Ld++
lcl|NCBI__GCF_000025485.1:WP_012971451.1 7 LGFPRIGAKRELKFALESYWKGESTLDTLRAVGAELRARHWQAQA--DLDLVPVGDFAFYDQMLDMSFT 73
79***************************************9987..78******************** PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek..........kdvaalemtkwfntnYhYlvPelskeeef 128
lg++p+r++ l++++ ldtyF++aRG + ++vaa emtkwf+tnYhY+vPe+++++ef
lcl|NCBI__GCF_000025485.1:WP_012971451.1 74 LGHLPKRVHGLKGES--LDTYFRVARGRSApaaeaqagctDGVAAGEMTKWFDTNYHYIVPEFTAATEF 140
**********96665..9*********9989********999*************************** PP
TIGR01371 129 klsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagve 197
kl++++lle++ eak++gv++kPv++Gp+t+l L+k+k+ +++l+ll++llpvY e+l++la++gv+
lcl|NCBI__GCF_000025485.1:WP_012971451.1 141 KLDASRLLEQLAEAKRQGVNAKPVIIGPVTYLALGKSKD--GSDRLALLDRLLPVYAELLNTLAAHGVQ 207
**************************************8..5699************************ PP
TIGR01371 198 wvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveak 266
wvqideP+lv++l++++++a++ ay+el+ + +klll+tYf++++++ +++lpv++l++D v+++
lcl|NCBI__GCF_000025485.1:WP_012971451.1 208 WVQIDEPILVTELDETWRHAFEIAYHELKT--APVKLLLATYFGELQDQRYLAAHLPVAGLHIDAVRGR 274
****************************97..699********************************** PP
TIGR01371 267 eelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleek 335
++l + + ++++k+L++GvidGrniwk+dl+++l+ l+ ++++ g++l++++scsllhvpvdl+ e++
lcl|NCBI__GCF_000025485.1:WP_012971451.1 275 DDLVALLNLLPSSKILSLGVIDGRNIWKTDLNAVLDWLEPIQDQLGERLWIAPSCSLLHVPVDLDSERT 343
**999999************************************************************* PP
TIGR01371 336 ldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekk 403
ld+e++++lafa++kl+el+vl++al++ ++av ++l+a++aai +r++s+rv+d +vk++l+ ++++
lcl|NCBI__GCF_000025485.1:WP_012971451.1 344 LDPEIRSWLAFARQKLNELRVLATALNQgREAVRAELDANRAAIDSRRQSPRVNDPEVKASLTRIDARL 412
****************************9**************************************** PP
TIGR01371 404 arressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklq 472
rr+s++++Ra++q+ lnlP +PtttiGsfPqt e+R+aR++f++g+i+e++Y+++++ ei+++++ q
lcl|NCBI__GCF_000025485.1:WP_012971451.1 413 GRRQSPYADRAAKQAGLLNLPEFPTTTIGSFPQTGEIRQARRQFKAGTIDEATYVEIMRGEIARCVREQ 481
********************************************************************* PP
TIGR01371 473 eelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaq 541
e+lglDvLvhGe+eRnDmveyFge+laGf+f q+gWvqsYGsRcvkPpi++gd+ rpk+mtv++++yaq
lcl|NCBI__GCF_000025485.1:WP_012971451.1 482 EALGLDVLVHGEAERNDMVEYFGEQLAGFTFSQFGWVQSYGSRCVKPPILFGDIRRPKAMTVDWITYAQ 550
********************************************************************* PP
TIGR01371 542 sltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlr 610
slt+kp+kGmLtGPvtilnWsfvR+D+pr+ +++q+ala+r+ev dLe ag+++iqiDe+alReglPlr
lcl|NCBI__GCF_000025485.1:WP_012971451.1 551 SLTDKPMKGMLTGPVTILNWSFVRDDQPRSVSCRQLALAMREEVLDLERAGVRVIQIDEAALREGLPLR 619
********************************************************************* PP
TIGR01371 611 ksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalke 679
+s++++Yldwave Fr++a+gv+d+tqihthmCYsefn+ii++ia++daDvi+ie+srsdmellda+++
lcl|NCBI__GCF_000025485.1:WP_012971451.1 620 RSQWTDYLDWAVECFRITANGVSDATQIHTHMCYSEFNDIIASIADMDADVITIETSRSDMELLDAFDD 688
********************************************************************* PP
TIGR01371 680 ikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaa 748
++y++ iG+GvyDihsp++P + ++ el++ka +++p++rlWvnPDCGLktR+w+ev++al+n+v+aa
lcl|NCBI__GCF_000025485.1:WP_012971451.1 689 -FSYPNAIGPGVYDIHSPNIPGEAHMVELMRKAAERIPAQRLWVNPDCGLKTRQWSEVIPALTNMVAAA 756
.66****************************************************************** PP
TIGR01371 749 kelRe 753
k+lR+
lcl|NCBI__GCF_000025485.1:WP_012971451.1 757 KTLRA 761
***97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (764 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 11.04
//
[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