Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_013819719.1 METME_RS15650 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000214665.1:WP_013819719.1
Length = 763
Score = 868 bits (2244), Expect = 0.0
Identities = 449/760 (59%), Positives = 549/760 (72%), Gaps = 19/760 (2%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G +RELK A E+YW G S+R++L +G++LR RHW Q Q+G+D +PVGDFA
Sbjct: 5 HNLGFPRIGAKRELKFALEAYWKGESSRDDLKTLGQQLRQRHW--QLQSGLDWVPVGDFA 62
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEP-------AAAAEMTKW 118
+YD VL S LGN+P R Q+ G +D FR+ RGR+ AA EMTKW
Sbjct: 63 FYDQVLDMSFTLGNLPERVQDFHGDA-LDNYFRVARGRSAQSASNAQCCGGVAAGEMTKW 121
Query: 119 FNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQF 178
F+TNYHY+VPEF +FKL ++LL+++ EA A G VKPV++GPVT+LWLGK K +
Sbjct: 122 FDTNYHYIVPEFTAATEFKLDASRLLEQLAEAKAQGVTVKPVIIGPVTYLWLGKAKDDS- 180
Query: 179 DRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVK 237
++L+LL +LPVY ++L LA +G+EWVQIDEP LV EL W A+ AY LQ +VK
Sbjct: 181 NKLALLPKLLPVYAELLETLAAQGVEWVQIDEPILVTELDAEWRHAFNTAYHNLQDSRVK 240
Query: 238 LLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVW 297
LLL TYF + N + LPV GLHVD V+G+DD+ L RL +D +LS G+INGRN+W
Sbjct: 241 LLLATYFGQLAENRNLAANLPVAGLHVDAVNGRDDIEPLIIRLSADKVLSLGVINGRNIW 300
Query: 298 RADLTEKYAQIKDI---VGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCH 354
+ DL ++ I +G+R LW+A SCSLLH P+DL E +LDAE+KSW AFA QK
Sbjct: 301 KTDLNAVLDWLEPIAQQLGER-LWLAPSCSLLHVPVDLDSEQKLDAEIKSWLAFAKQKLG 359
Query: 355 ELALLRDALNSGDTAALAEWSA---PIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYE 411
EL +L ALN G A AE A I+ARR+S+RV+NPAV+ LA I A+ QR + Y
Sbjct: 360 ELQVLATALNRGRDAVKAELDANRAAIKARRNSSRVNNPAVKAALAKIDAKLGQRQSSYA 419
Query: 412 VRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVE 471
RA Q A KLP +PTTTIGSFPQT+EIR R FK G LDA Y+ + I + + E
Sbjct: 420 QRALKQAALLKLPKFPTTTIGSFPQTSEIRLARSQFKSGKLDAAGYKAAMRAEIARCVRE 479
Query: 472 QERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAP 531
QE LGLDV VHGEAERNDMVEYFGE L+G+ F+Q+GWVQSYGSRCVKPPI+ GDISRP P
Sbjct: 480 QEALGLDVFVHGEAERNDMVEYFGEQLNGYAFSQSGWVQSYGSRCVKPPILFGDISRPQP 539
Query: 532 ITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAA 591
+TVEW YAQSLTD P+KGMLTGPVTIL WSF R+D R KQ+ALA+R+EV DLE A
Sbjct: 540 MTVEWISYAQSLTDTPMKGMLTGPVTILNWSFVRDDQPRSVTCKQLALAIREEVLDLEKA 599
Query: 592 GIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIM 651
GIG+IQIDE ALREGLPLR+S W YL W VE+FRI A D+TQIHTHMCY EFNDI+
Sbjct: 600 GIGVIQIDEAALREGLPLRKSQWQEYLDWAVESFRITANGVADETQIHTHMCYSEFNDII 659
Query: 652 DSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKA 711
+IA +DAD ITIETSRSDMELL++FE F+YPN IGPGVYDIHSPN+PS + I AL+ KA
Sbjct: 660 AAIADMDADAITIETSRSDMELLDAFEHFNYPNGIGPGVYDIHSPNIPSEQHIVALMHKA 719
Query: 712 AKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
A+R+P E+LWVNPDCGLKTR W E AL NMV AA+ LR
Sbjct: 720 AERVPTEQLWVNPDCGLKTRQWAEVIPALTNMVAAAKTLR 759
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: 1735
Number of extensions: 83
Number of successful extensions: 9
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: 763
Length adjustment: 40
Effective length of query: 713
Effective length of database: 723
Effective search space: 515499
Effective search space used: 515499
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_013819719.1 METME_RS15650 (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.2938.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 1120.3 0.0 0 1120.1 0.0 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013819719.1 METME_RS15650 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013819719.1 METME_RS15650 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1120.1 0.0 0 0 1 753 [. 7 760 .. 7 761 .. 0.99
Alignments for each domain:
== domain 1 score: 1120.1 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+kRelk+ale+ywkg++s+++l++ ++lr+++++ q+ g+d +pv+df++YD+vLd++
lcl|NCBI__GCF_000214665.1:WP_013819719.1 7 LGFPRIGAKRELKFALEAYWKGESSRDDLKTLGQQLRQRHWQLQS--GLDWVPVGDFAFYDQVLDMSFT 73
79****************************************998..9********************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek.........kdvaalemtkwfntnYhYlvPelskeeefk 129
lg++per+++ ++d+ ld+yF++aRG + +vaa emtkwf+tnYhY+vPe+++++efk
lcl|NCBI__GCF_000214665.1:WP_013819719.1 74 LGNLPERVQDFHGDA--LDNYFRVARGRSAqsasnaqccGGVAAGEMTKWFDTNYHYIVPEFTAATEFK 140
**********97776..9*********98899******999**************************** PP
TIGR01371 130 lsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvew 198
l++++lle++ eak++gv +kPv++Gp+t+l+L+kak+ ++++l+ll+kllpvY e+l++la++gvew
lcl|NCBI__GCF_000214665.1:WP_013819719.1 141 LDASRLLEQLAEAKAQGVTVKPVIIGPVTYLWLGKAKD--DSNKLALLPKLLPVYAELLETLAAQGVEW 207
*************************************8..5689************************* PP
TIGR01371 199 vqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveake 267
vqideP+lv++l++e+++a+++ay++l++ +++klll+tYf+++ e+ + +++lpv++l++D v++++
lcl|NCBI__GCF_000214665.1:WP_013819719.1 208 VQIDEPILVTELDAEWRHAFNTAYHNLQD--SRVKLLLATYFGQLAENRNLAANLPVAGLHVDAVNGRD 274
****************************8..79************************************ PP
TIGR01371 268 elelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekl 336
+ e ++++dkvL++Gvi+Grniwk+dl+++l+ l+ ++++ g++l++++scsllhvpvdl+ e+kl
lcl|NCBI__GCF_000214665.1:WP_013819719.1 275 DIEPLIIRLSADKVLSLGVINGRNIWKTDLNAVLDWLEPIAQQLGERLWLAPSCSLLHVPVDLDSEQKL 343
********************************************************************* PP
TIGR01371 337 dkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekka 404
d+e+k++lafak+kl el+vl++al+ ++av+++l+a++aai+ar++s+rv++ +vk++l+++++k
lcl|NCBI__GCF_000214665.1:WP_013819719.1 344 DAEIKSWLAFAKQKLGELQVLATALNRgRDAVKAELDANRAAIKARRNSSRVNNPAVKAALAKIDAKLG 412
**************************99***************************************** PP
TIGR01371 405 rressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqe 473
+r+ss+++Ra +q++ l+lP +PtttiGsfPqt+e+R aR++f+ g+++++ Y++++++ei+++++ qe
lcl|NCBI__GCF_000214665.1:WP_013819719.1 413 QRQSSYAQRALKQAALLKLPKFPTTTIGSFPQTSEIRLARSQFKSGKLDAAGYKAAMRAEIARCVREQE 481
********************************************************************* PP
TIGR01371 474 elglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqs 542
+lglDv vhGe+eRnDmveyFge+l+G+af q+gWvqsYGsRcvkPpi++gd+srp+pmtv+++ yaqs
lcl|NCBI__GCF_000214665.1:WP_013819719.1 482 ALGLDVFVHGEAERNDMVEYFGEQLNGYAFSQSGWVQSYGSRCVKPPILFGDISRPQPMTVEWISYAQS 550
********************************************************************* PP
TIGR01371 543 ltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrk 611
lt+ p+kGmLtGPvtilnWsfvR+D+pr+ +++q+ala+r+ev dLe+agi +iqiDe+alReglPlrk
lcl|NCBI__GCF_000214665.1:WP_013819719.1 551 LTDTPMKGMLTGPVTILNWSFVRDDQPRSVTCKQLALAIREEVLDLEKAGIGVIQIDEAALREGLPLRK 619
********************************************************************* PP
TIGR01371 612 sdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkei 680
s+++eYldwave+Fr++a+gv+detqihthmCYsefn+ii+aia++daD i+ie+srsdmellda+++
lcl|NCBI__GCF_000214665.1:WP_013819719.1 620 SQWQEYLDWAVESFRITANGVADETQIHTHMCYSEFNDIIAAIADMDADAITIETSRSDMELLDAFEH- 687
********************************************************************. PP
TIGR01371 681 kkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaak 749
++y+++iG+GvyDihsp++Ps++++ +l++ka +++p+e+lWvnPDCGLktR+w ev++al+n+v+aak
lcl|NCBI__GCF_000214665.1:WP_013819719.1 688 FNYPNGIGPGVYDIHSPNIPSEQHIVALMHKAAERVPTEQLWVNPDCGLKTRQWAEVIPALTNMVAAAK 756
77******************************************************************* PP
TIGR01371 750 elRe 753
+lR+
lcl|NCBI__GCF_000214665.1:WP_013819719.1 757 TLRA 760
**97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (763 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: 00:00:00.04
# Mc/sec: 12.16
//
[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