Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_013010913.1 DACET_RS08195 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000025725.1:WP_013010913.1
Length = 755
Score = 726 bits (1873), Expect = 0.0
Identities = 369/754 (48%), Positives = 497/754 (65%), Gaps = 12/754 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G RELKKA E YW T + L G ELR +HW QK +G+ + GDF+
Sbjct: 4 HILGFPRIGKNRELKKALELYWKKEITLQNLQQTGSELRKQHWKIQKDSGLSYVTTGDFS 63
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
+YDHVL S+++G VP R + G D+D F++ RG A + +A EMTKWF+TNYHY
Sbjct: 64 FYDHVLDVSMMIGAVPERFKISAGESDLDVYFKMARGDAFS--QVSAMEMTKWFDTNYHY 121
Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
+VPE K + ++D+ EA+ G+ KPVLLGPVT+L L K + FD+ L +
Sbjct: 122 IVPELSDSTVLKFSGRDIIDQTCEAVDAGYDAKPVLLGPVTYLSLSK-SVDGFDKWLLAD 180
Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQV---KLLLTT 242
+ +Y QV+AEL+ WVQ+DEP L ++ +A+K Y L +LLTT
Sbjct: 181 KLGDIYVQVIAELSSM-CRWVQVDEPILCADMELEAAEAFKKIYKKLNSSPDSGSILLTT 239
Query: 243 YFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLT 302
YF+ + N D GLH+DL+ G + LP LS G+++GRN+W DL
Sbjct: 240 YFDNLDDNADLALNSGCTGLHIDLIRGGGAAEHIVNNLPDFMTLSVGVVDGRNIWTTDLV 299
Query: 303 EKYAQIKDIVGK---RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALL 359
+ Q+++I K L + SSCSLLHSP+D++ E +D+E+K+W +FA+QKC E ALL
Sbjct: 300 KARKQLENIKEKVPHERLMIGSSCSLLHSPVDITSEAGIDSELKTWMSFAVQKCRETALL 359
Query: 360 RDALNSGDTAALAEWSAPI-QARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQR 418
++ G+ + E + I ++R S++VH+ V++ I + +R + Y R + Q
Sbjct: 360 GAVMSGGEYSREIEHNQEIIRSRNESSKVHSAKVKELTECIDSSMLKRKSPYSKRKKEQ- 418
Query: 419 ARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLD 478
LP +PTTTIGSFPQT EIR R F+ G + +Y I IK+ I +QE L LD
Sbjct: 419 GWLNLPLFPTTTIGSFPQTDEIRNQRRKFRNGEVFIEDYDFFIRNEIKKIIRKQEELNLD 478
Query: 479 VLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAK 538
VLVHGE ERNDMVEYFG+ + GF FTQNGWVQSYGSRCVKPP++ GD+ R +TV+W
Sbjct: 479 VLVHGEPERNDMVEYFGQKMHGFCFTQNGWVQSYGSRCVKPPVIYGDVFRRGDMTVDWIT 538
Query: 539 YAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQI 598
YAQSLT KPVKGMLTGPVTILCWSF R+D+ + + +QIALA+R+EV LE AGI IIQI
Sbjct: 539 YAQSLTGKPVKGMLTGPVTILCWSFVRDDIEKAEVCRQIALAVREEVMSLEKAGINIIQI 598
Query: 599 DEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALD 658
DE A EG+P++ D + Y +W +AFR+ ++ +D TQIHTHMCY EFN+I+++IA +D
Sbjct: 599 DEAAFSEGMPVKHKDRNGYFRWATDAFRLASSGVQDKTQIHTHMCYSEFNEIIEAIADMD 658
Query: 659 ADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAE 718
ADVI+IE+SRS M LL++F +F+YP +IGPGVYDIHSP VPSVE I+ L+ A ++IPAE
Sbjct: 659 ADVISIESSRSGMVLLDAFNDFEYPRDIGPGVYDIHSPRVPSVEEIKGLISSALEKIPAE 718
Query: 719 RLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
RLW+NPDCGLKTR W E +L NMVQA + +RR
Sbjct: 719 RLWINPDCGLKTREWREVMESLHNMVQAVKEIRR 752
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: 1518
Number of extensions: 67
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: 753
Length of database: 755
Length adjustment: 40
Effective length of query: 713
Effective length of database: 715
Effective search space: 509795
Effective search space used: 509795
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_013010913.1 DACET_RS08195 (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.25635.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 1050.0 0.0 0 1049.8 0.0 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013010913.1 DACET_RS08195 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013010913.1 DACET_RS08195 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1049.8 0.0 0 0 1 754 [] 6 753 .. 6 753 .. 0.99
Alignments for each domain:
== domain 1 score: 1049.8 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig++Relkkale ywk++i+ ++l+++ ++lrk+++k qk++g+ +++++dfs+YDhvLd++++
lcl|NCBI__GCF_000025725.1:WP_013010913.1 6 LGFPRIGKNRELKKALELYWKKEITLQNLQQTGSELRKQHWKIQKDSGLSYVTTGDFSFYDHVLDVSMM 74
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknkllee 138
+ga+perfk + +esdld+yF++aRG++ ++v+a+emtkwf+tnYhY+vPels+++ +k+s + ++++
lcl|NCBI__GCF_000025725.1:WP_013010913.1 75 IGAVPERFKIS-AGESDLDVYFKMARGDAFSQVSAMEMTKWFDTNYHYIVPELSDSTVLKFSGRDIIDQ 142
*********98.5556***************************************************** PP
TIGR01371 139 ykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlv 207
ea +g ++kPvllGp+t+l+L+k+++ +++ l +kl ++Y +v+ +l++ ++wvq+deP+l
lcl|NCBI__GCF_000025725.1:WP_013010913.1 143 TCEAVDAGYDAKPVLLGPVTYLSLSKSVD--GFDKWLLADKLGDIYVQVIAELSS-MCRWVQVDEPILC 208
****************************8..789999****************98.89*********** PP
TIGR01371 208 ldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakf 276
d++ e+ +a+k++y++l+++ + ++ll+tYfd+++++ + +++ ++l++Dl+++ +e ++++
lcl|NCBI__GCF_000025725.1:WP_013010913.1 209 ADMELEAAEAFKKIYKKLNSSPDSGSILLTTYFDNLDDNADLALNSGCTGLHIDLIRGGGAAEHIVNNL 277
********************************************************************* PP
TIGR01371 277 eedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvpvdleleekldkelkell 344
++ +L++Gv+dGrniw +dl k+ k+l+++++k+ ++l++ +scsllh+pvd++ e +d+elk+++
lcl|NCBI__GCF_000025725.1:WP_013010913.1 278 PDFMTLSVGVVDGRNIWTTDLVKARKQLENIKEKVPhERLMIGSSCSLLHSPVDITSEAGIDSELKTWM 346
*********************************9988******************************** PP
TIGR01371 345 afakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeR 413
+fa++k++e ++l +++g + + ++e++++ i++r++s++v+++kvke e +++++ +r+s++++R
lcl|NCBI__GCF_000025725.1:WP_013010913.1 347 SFAVQKCRETALLGAVMSG-GEYSREIEHNQEIIRSRNESSKVHSAKVKELTECIDSSMLKRKSPYSKR 414
*****************99.778899999999************************************* PP
TIGR01371 414 aeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvh 482
+++q lnlPl+PtttiGsfPqt e+R++R+kfr+ge+ e+Y+ fi++eikk+i+ qeel+lDvLvh
lcl|NCBI__GCF_000025725.1:WP_013010913.1 415 KKEQG-WLNLPLFPTTTIGSFPQTDEIRNQRRKFRNGEVFIEDYDFFIRNEIKKIIRKQEELNLDVLVH 482
99985.8************************************************************** PP
TIGR01371 483 GefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGm 551
Ge+eRnDmveyFg k++Gf ftqngWvqsYGsRcvkPp+iygdv r mtv++++yaqslt kpvkGm
lcl|NCBI__GCF_000025725.1:WP_013010913.1 483 GEPERNDMVEYFGQKMHGFCFTQNGWVQSYGSRCVKPPVIYGDVFRRGDMTVDWITYAQSLTGKPVKGM 551
********************************************************************* PP
TIGR01371 552 LtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldw 620
LtGPvtil+WsfvR+D++++e+++qiala+r+ev Le+agi+iiqiDe+a+ eg+P++++d++ Y++w
lcl|NCBI__GCF_000025725.1:WP_013010913.1 552 LTGPVTILCWSFVRDDIEKAEVCRQIALAVREEVMSLEKAGINIIQIDEAAFSEGMPVKHKDRNGYFRW 620
********************************************************************* PP
TIGR01371 621 aveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGl 689
a +aFrla+sgv+d+tqihthmCYsefneiieaia++daDvisie srs m llda+++ ++y+++iG+
lcl|NCBI__GCF_000025725.1:WP_013010913.1 621 ATDAFRLASSGVQDKTQIHTHMCYSEFNEIIEAIADMDADVISIESSRSGMVLLDAFND-FEYPRDIGP 688
***********************************************************.67******* PP
TIGR01371 690 GvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
GvyDihsprvPs+ee++ l+++al+k+p+erlW+nPDCGLktR+w ev ++l+n+v+a+ke+R +
lcl|NCBI__GCF_000025725.1:WP_013010913.1 689 GVYDIHSPRVPSVEEIKGLISSALEKIPAERLWINPDCGLKTREWREVMESLHNMVQAVKEIRRQ 753
**************************************************************975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (755 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.05
# Mc/sec: 9.64
//
[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