Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate CA265_RS21095 CA265_RS21095 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__Pedo557:CA265_RS21095
Length = 777
Score = 791 bits (2043), Expect = 0.0
Identities = 404/766 (52%), Positives = 526/766 (68%), Gaps = 17/766 (2%)
Query: 3 ILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVG 62
+L LG+PR+G +RELKK E+YWA + + +L VG+ +R +W+ QK+AGID++P
Sbjct: 1 MLTQNLGYPRIGSQRELKKICENYWADKTGYKNVLQVGKNIRHENWNLQKEAGIDVIPSN 60
Query: 63 DFAWYDHVLTTSLLLGNVPARHQN---KDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWF 119
DF++YDHVL SL G +P R+ K G+ ++D F + RG G A EMTKWF
Sbjct: 61 DFSFYDHVLDHSLTFGAIPKRYNEVILKKGNSELDLYFAMARGYQKEGLDVVAMEMTKWF 120
Query: 120 NTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFD 179
+TNYHY+VPEF K Q FKL T+++DE EA LG KPVL+GPV++L LGK K F+
Sbjct: 121 DTNYHYIVPEFYKDQPFKLFSTKVIDEFYEAKQLGITTKPVLIGPVSYLLLGKEKEAGFE 180
Query: 180 RLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQG---QV 236
++ L+ ++LPVY ++L+ L +E+VQ DEP L L+L AY+ Y ++ ++
Sbjct: 181 KIDLIKNLLPVYIEILSRLDALDVEYVQFDEPFLTLDLTDKDKKAYEYVYKEIRKTFPRL 240
Query: 237 KLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNV 296
K++L TYFEG+ NL T+LPV LH+DLV +D ++ + L + +LS GL++GRN+
Sbjct: 241 KIVLATYFEGLGNNLALTTSLPVNVLHIDLVRAEDQLSAVLASLKEETILSLGLVDGRNI 300
Query: 297 WRADLTEKYAQIKDIVGKRDL---WVASSCSLLHSPIDLSVETR---LDAEVKSWFAFAL 350
W+ D + + I +V KR L W+A SCSL+HSP+DL ET L AE+K W A++
Sbjct: 301 WKNDFEKSVSIINQVVEKRGLDKVWIAPSCSLIHSPVDLDNETNEQNLSAEIKQWLAYSK 360
Query: 351 QKCHELALLRDALNSGDTAA----LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQR 406
QK ELA L+ + + A+ L E I R+ S +HNP V++R+ + AQD++R
Sbjct: 361 QKISELATLKKLITNESPASTLQKLEENKIAIANRKVSKIIHNPEVKERVLGLKAQDAER 420
Query: 407 ANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIK 466
+ + R Q+ LP + TTTIGSFPQT E+R+ R K G Y IA+
Sbjct: 421 LSPFSSRKIKQQ-ELNLPIYATTTIGSFPQTAEVRSWRAKLKNGTFTVEEYDDLIAKETA 479
Query: 467 QAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDI 526
+A+ QE + LDVLVHGE ERNDMVEYFGE LDGF F++NGWVQSYGSRCVKPPI+ GD+
Sbjct: 480 KAVNWQEEIDLDVLVHGEFERNDMVEYFGEQLDGFAFSKNGWVQSYGSRCVKPPIIFGDV 539
Query: 527 SRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVA 586
SRP P+TV+W YAQSLT K +KGMLTGPVTIL WSF R D R QIALA+RDEV
Sbjct: 540 SRPKPMTVKWTAYAQSLTSKYMKGMLTGPVTILQWSFVRNDQPRSETCTQIALAIRDEVC 599
Query: 587 DLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCE 646
DLE AGI IIQIDEPA+REGLPLR++DW YL W V+AF+I+A+ KDDTQIHTHMCY E
Sbjct: 600 DLENAGIKIIQIDEPAIREGLPLRKADWQNYLNWAVKAFKISASGVKDDTQIHTHMCYSE 659
Query: 647 FNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEA 706
FNDI+ +IA +DADVITIETSRS MELL++F +F YPNEIGPGVYDIHSP VP E +
Sbjct: 660 FNDIIQNIADMDADVITIETSRSQMELLDAFADFKYPNEIGPGVYDIHSPRVPKREEMVQ 719
Query: 707 LLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
LLKKA IP E+LWVNPDCGLKTRGW ET+ AL MV+AA+ +R+
Sbjct: 720 LLKKAKAVIPPEQLWVNPDCGLKTRGWDETKKALIEMVEAAKEMRK 765
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: 1577
Number of extensions: 84
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: 777
Length adjustment: 40
Effective length of query: 713
Effective length of database: 737
Effective search space: 525481
Effective search space used: 525481
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 CA265_RS21095 CA265_RS21095 (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.1683.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 1120.6 1.6 0 1120.4 1.6 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS21095 CA265_RS21095 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS21095 CA265_RS21095 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methy
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1120.4 1.6 0 0 1 753 [. 6 765 .. 6 766 .. 0.98
Alignments for each domain:
== domain 1 score: 1120.4 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtav 68
lg+Prig++Relkk e+yw++k+ +++l+v k++r+++++ qkeag+dvip+ndfs+YDhvLd ++
lcl|FitnessBrowser__Pedo557:CA265_RS21095 6 LGYPRIGSQRELKKICENYWADKTGYKNVLQVGKNIRHENWNLQKEAGIDVIPSNDFSFYDHVLDHSL 73
79****************************************************************** PP
TIGR01371 69 llgaiperfkel..addesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsk 132
+gaip+r++e+ ++++s+ld yFa+aRG++k dv+a+emtkwf+tnYhY+vPe+ k++ fkl +
lcl|FitnessBrowser__Pedo557:CA265_RS21095 74 TFGAIPKRYNEVilKKGNSELDLYFAMARGYQKegLDVVAMEMTKWFDTNYHYIVPEFYKDQPFKLFS 141
**********9733456778***********9966689****************************** PP
TIGR01371 133 nklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvq 200
+k+++e+ eak+lg+ tkPvl+Gp+++l+L+k+ke +e+ +l+++llpvY e+l++l++ +ve+vq
lcl|FitnessBrowser__Pedo557:CA265_RS21095 142 TKVIDEFYEAKQLGITTKPVLIGPVSYLLLGKEKE-AGFEKIDLIKNLLPVYIEILSRLDALDVEYVQ 208
*********************************96.88****************************** PP
TIGR01371 201 idePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee 268
+deP l ldl++++++a++ +y+e++++ +lk++l+tYf+ + ++l+ ++slpv+ l++Dlv+a+++
lcl|FitnessBrowser__Pedo557:CA265_RS21095 209 FDEPFLTLDLTDKDKKAYEYVYKEIRKTFPRLKIVLATYFEGLGNNLALTTSLPVNVLHIDLVRAEDQ 276
******************************************************************** PP
TIGR01371 269 lelakakfeedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvpvdlele.. 333
l+++ a+++e+ +L++G++dGrniwk+d+eks+++++++ +k+g dk+++++scsl+h+pvdl++e
lcl|FitnessBrowser__Pedo557:CA265_RS21095 277 LSAVLASLKEETILSLGLVDGRNIWKNDFEKSVSIINQVVEKRGlDKVWIAPSCSLIHSPVDLDNEtn 344
***************************************************************97521 PP
TIGR01371 334 .ekldkelkellafakekleelkvlkealeg..eaavaealeaeaaaiaarkkskrvadekvkerlea 398
++l++e+k++la++k+k++el++lk+++++ a++ ++le+++ aia+rk sk++++ +vker+
lcl|FitnessBrowser__Pedo557:CA265_RS21095 345 eQNLSAEIKQWLAYSKQKISELATLKKLITNesPASTLQKLEENKIAIANRKVSKIIHNPEVKERVLG 412
168*************************988555788899**************************** PP
TIGR01371 399 lkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeik 466
lk+++a+r s+f+ R+ +q++ lnlP++ tttiGsfPqt+evR+ Rak+++g+++ eeY++ i +e++
lcl|FitnessBrowser__Pedo557:CA265_RS21095 413 LKAQDAERLSPFSSRKIKQQE-LNLPIYATTTIGSFPQTAEVRSWRAKLKNGTFTVEEYDDLIAKETA 479
***************998875.9********************************************* PP
TIGR01371 467 kviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtv 534
k++++qee++lDvLvhGefeRnDmveyFge+l+Gfaf +ngWvqsYGsRcvkPpii+gdvsrpkpmtv
lcl|FitnessBrowser__Pedo557:CA265_RS21095 480 KAVNWQEEIDLDVLVHGEFERNDMVEYFGEQLDGFAFSKNGWVQSYGSRCVKPPIIFGDVSRPKPMTV 547
******************************************************************** PP
TIGR01371 535 keskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepa 602
k+++yaqsltsk +kGmLtGPvtil+WsfvR+D+pr+e+++qiala+rdev dLe+agikiiqiDepa
lcl|FitnessBrowser__Pedo557:CA265_RS21095 548 KWTAYAQSLTSKYMKGMLTGPVTILQWSFVRNDQPRSETCTQIALAIRDEVCDLENAGIKIIQIDEPA 615
******************************************************************** PP
TIGR01371 603 lReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsd 670
+ReglPlrk+d+++Yl+wav+aF+++asgvkd+tqihthmCYsefn+ii++ia++daDvi+ie+srs+
lcl|FitnessBrowser__Pedo557:CA265_RS21095 616 IREGLPLRKADWQNYLNWAVKAFKISASGVKDDTQIHTHMCYSEFNDIIQNIADMDADVITIETSRSQ 683
******************************************************************** PP
TIGR01371 671 melldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevk 738
mellda+ + +ky++eiG+GvyDihsprvP ee+ +ll+ka +++p e+lWvnPDCGLktR w+e+k
lcl|FitnessBrowser__Pedo557:CA265_RS21095 684 MELLDAFAD-FKYPNEIGPGVYDIHSPRVPKREEMVQLLKKAKAVIPPEQLWVNPDCGLKTRGWDETK 750
*********.77******************************************************** PP
TIGR01371 739 aalknlveaakelRe 753
+al ++veaake+R+
lcl|FitnessBrowser__Pedo557:CA265_RS21095 751 KALIEMVEAAKEMRK 765
*************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (777 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: 00:00:00.04
# Mc/sec: 12.46
//
[ok]
This GapMind analysis is from Apr 09 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