Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate RR42_RS30660 RR42_RS30660 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__Cup4G11:RR42_RS30660
Length = 795
Score = 848 bits (2191), Expect = 0.0
Identities = 438/753 (58%), Positives = 532/753 (70%), Gaps = 12/753 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H GFPR+G +RELK AQE++W G + L V LR RHW Q QAG+D + VGDFA
Sbjct: 5 HIAGFPRIGAQRELKFAQEAFWRGETDEASLRQVATGLRQRHWQSQAQAGLDSVAVGDFA 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
+YD VL S LLG +PAR + + F + RG + A EMTKWF+TNYHY
Sbjct: 65 YYDQVLGLSALLGALPARFGFDPKQLSLAQYFELARGN----KAQPAMEMTKWFDTNYHY 120
Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
+VPE +F DEV+EALALG K KPVL+GPVT+LWL K + FDRLSLL
Sbjct: 121 LVPELGPDTRFDGGVDWFFDEVEEALALGLKAKPVLIGPVTYLWLSKTHVDGFDRLSLLP 180
Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDAL-QGQVKLLLTTYF 244
++ Y ++LA L RGIEWVQIDEPAL L+L AWLDAY AY L + VKLLL TYF
Sbjct: 181 SLVAAYGRILARLRDRGIEWVQIDEPALCLDLEPAWLDAYDGAYAELAKSGVKLLLATYF 240
Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEK 304
+ + ALPV G H+DLV + K LP+ +LSAG+I+GRN+WR DL
Sbjct: 241 DNAADHAARAAALPVHGFHIDLVRAPQQLDAWRKVLPAGAVLSAGVIDGRNIWRTDLRRA 300
Query: 305 YAQIKDI---VGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRD 361
+ + + +G+R LWVA SCSLLH P+ L E +LDA++K+W AFA +K E+++L
Sbjct: 301 LSVLAPLHAELGER-LWVAPSCSLLHVPVSLEAERKLDAQIKTWLAFATEKLAEVSVLAR 359
Query: 362 ALNSGDTAA---LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQR 418
ALN G+ A LA A + +RR S+RV N V+ R+AA+TA +QR + ++ R E QR
Sbjct: 360 ALNEGEAAVAPELAAADAALASRRSSSRVVNQQVQARVAAVTAAMAQRKSPFQTRIERQR 419
Query: 419 ARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLD 478
+LPA PTTTIGSFPQTT IR R +++G + A Y I I+ A+ +QE LGLD
Sbjct: 420 TALQLPALPTTTIGSFPQTTAIRQTRAAYRRGEIGALEYLQRIRGEIETAVRKQEALGLD 479
Query: 479 VLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAK 538
VLVHGEAERNDMVEYFGE L G+ FT+NGWVQSYGSRCVKPP++ GD+ RP P+TVE +
Sbjct: 480 VLVHGEAERNDMVEYFGEQLCGYTFTENGWVQSYGSRCVKPPVIYGDVYRPEPMTVETTR 539
Query: 539 YAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQI 598
YAQSLT++P+KGMLTGPVT+L WSF R+D R T Q+ALA+RDEV+DLE AGI IIQI
Sbjct: 540 YAQSLTERPMKGMLTGPVTMLQWSFVRDDQPRATTTLQLALAIRDEVSDLEQAGIRIIQI 599
Query: 599 DEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALD 658
DEPALREGLPLR+ DW AYL W V AF+I+AA +D TQIHTHMCY EFNDI+ +IAALD
Sbjct: 600 DEPALREGLPLRKGDWAAYLDWAVHAFKISAASVEDQTQIHTHMCYAEFNDILPAIAALD 659
Query: 659 ADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAE 718
ADVITIETSRS MELLE F EFDYPNEIGPGVYDIHSP VPSVE I LL++A + IP +
Sbjct: 660 ADVITIETSRSAMELLEGFGEFDYPNEIGPGVYDIHSPRVPSVEAITHLLERACEVIPPQ 719
Query: 719 RLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
RLWVNPDCGLKTR WPET AALANMV AA+ LR
Sbjct: 720 RLWVNPDCGLKTRAWPETEAALANMVAAARGLR 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: 1710
Number of extensions: 82
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: 795
Length adjustment: 41
Effective length of query: 712
Effective length of database: 754
Effective search space: 536848
Effective search space used: 536848
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 RR42_RS30660 RR42_RS30660 (5-methyltetrahydropteroyltriglutamate-- homocysteine 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.23624.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 1094.8 0.0 0 1094.6 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS30660 RR42_RS30660 5-methyltetrahydrop
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS30660 RR42_RS30660 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1094.6 0.0 0 0 2 754 .] 8 754 .. 7 754 .. 0.99
Alignments for each domain:
== domain 1 score: 1094.6 bits; conditional E-value: 0
TIGR01371 2 gfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavll 70
gfPrig++Relk+a+e++w+g++++++l +va+ lr++++++q++ag+d+++v+df++YD+vL +++ll
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 8 GFPRIGAQRELKFAQEAFWRGETDEASLRQVATGLRQRHWQSQAQAGLDSVAVGDFAYYDQVLGLSALL 76
9******************************************************************** PP
TIGR01371 71 gaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknklleey 139
ga+p+rf ++ +l++yF++aRG++ +a+emtkwf+tnYhYlvPel ++++f + ++e+
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 77 GALPARFGFD-PKQLSLAQYFELARGNKA--QPAMEMTKWFDTNYHYLVPELGPDTRFDGGVDWFFDEV 142
********97.55568**********955..89************************************ PP
TIGR01371 140 keakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvl 208
+ea +lg+++kPvl+Gp+t+l+L+k++ + +++l+ll++l+ +Y ++l +l+++g+ewvqideP+l l
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 143 EEALALGLKAKPVLIGPVTYLWLSKTHV-DGFDRLSLLPSLVAAYGRILARLRDRGIEWVQIDEPALCL 210
*************************996.78************************************** PP
TIGR01371 209 dlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfe 277
dl++++l+a+ ay+el++ + +klll+tYfd+ ++ + ++ lpv+++++Dlv+a+++l++ + ++
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 211 DLEPAWLDAYDGAYAELAK--SGVKLLLATYFDNAADHAARAAALPVHGFHIDLVRAPQQLDAWRKVLP 277
*****************97..79********************************************** PP
TIGR01371 278 edkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellaf 346
+ vL+aGvidGrniw++dl+++l++l+ l+a+ g++l+v++scsllhvpv+le+e+kld+++k++laf
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 278 AGAVLSAGVIDGRNIWRTDLRRALSVLAPLHAELGERLWVAPSCSLLHVPVSLEAERKLDAQIKTWLAF 346
********************************************************************* PP
TIGR01371 347 akekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRa 414
a+ekl+e++vl++al++ eaava +l+a++aa+a+r++s+rv +++v++r++a+++++a+r+s+f++R
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 347 ATEKLAEVSVLARALNEgEAAVAPELAAADAALASRRSSSRVVNQQVQARVAAVTAAMAQRKSPFQTRI 415
*****************9*************************************************** PP
TIGR01371 415 eaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhG 483
e q+ l+lP+lPtttiGsfPqt+ +R++Ra++r+gei + eY + i+ ei+ +++ qe+lglDvLvhG
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 416 ERQRTALQLPALPTTTIGSFPQTTAIRQTRAAYRRGEIGALEYLQRIRGEIETAVRKQEALGLDVLVHG 484
********************************************************************* PP
TIGR01371 484 efeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmL 552
e+eRnDmveyFge+l G++ft+ngWvqsYGsRcvkPp+iygdv rp+pmtv+ ++yaqslt++p+kGmL
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 485 EAERNDMVEYFGEQLCGYTFTENGWVQSYGSRCVKPPVIYGDVYRPEPMTVETTRYAQSLTERPMKGML 553
********************************************************************* PP
TIGR01371 553 tGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwa 621
tGPvt+l+WsfvR+D+pr++++ q+ala+rdev dLe+agi+iiqiDepalReglPlrk d+++Yldwa
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 554 TGPVTMLQWSFVRDDQPRATTTLQLALAIRDEVSDLEQAGIRIIQIDEPALREGLPLRKGDWAAYLDWA 622
********************************************************************* PP
TIGR01371 622 veaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlG 690
v+aF+++a++v+d+tqihthmCY+efn+i+ aiaaldaDvi+ie+srs mell+ + e ++y++eiG+G
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 623 VHAFKISAASVEDQTQIHTHMCYAEFNDILPAIAALDADVITIETSRSAMELLEGFGE-FDYPNEIGPG 690
**********************************************************.77******** PP
TIGR01371 691 vyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
vyDihsprvPs+e +++lle+a +++p +rlWvnPDCGLktR+w+e++aal n+v+aa+ lRe+
lcl|FitnessBrowser__Cup4G11:RR42_RS30660 691 VYDIHSPRVPSVEAITHLLERACEVIPPQRLWVNPDCGLKTRAWPETEAALANMVAAARGLREQ 754
**************************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (795 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 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 10.95
//
[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