Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate Pf1N1B4_783 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783
Length = 770
Score = 940 bits (2429), Expect = 0.0
Identities = 473/764 (61%), Positives = 568/764 (74%), Gaps = 16/764 (2%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
L HTLGFPR+G RELKKA E+YW G+ ++ L +VGR LRA HW QK AGIDLLPVGD
Sbjct: 3 LAHTLGFPRIGADRELKKALEAYWKGDLDQDALKSVGRHLRATHWQLQKDAGIDLLPVGD 62
Query: 64 FAWYDHVLTTSLLLGNVPARHQN-KD--GSVDIDTLFRIGRGRAPT---GEPAAAA---E 114
FAWYD VLT SL G +P R + KD G +DTLF + RG GE A E
Sbjct: 63 FAWYDQVLTHSLTFGVIPERFDSAKDERGLPTLDTLFAMARGATAACCGGEHTQAQYAQE 122
Query: 115 MTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVK 174
+TKWF+TNYHY+VPEF QQFKL+W QL DEVDEA ALGH VKPV++GP+T+LWLGK K
Sbjct: 123 LTKWFDTNYHYLVPEFTADQQFKLSWEQLFDEVDEAKALGHNVKPVIIGPLTYLWLGKAK 182
Query: 175 GEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ- 233
G FD+L LL +LP+Y ++L LA +G+EWVQIDEP L L+LPQAW +A++ AY LQ
Sbjct: 183 GNDFDKLDLLERLLPIYGEILGRLAAQGVEWVQIDEPILTLDLPQAWKNAFERAYHILQY 242
Query: 234 GQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLING 293
+K L+ TYF G+ NL +LPVQGLH+D V D + ++ RLP+ +LS GL+NG
Sbjct: 243 SPLKKLVATYFSGLEDNLGLAVSLPVQGLHIDAVRAPDQLGQVLDRLPTYKILSVGLVNG 302
Query: 294 RNVWRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQ 351
RNVWR +L + AQ++ + +LWV+SSCSLLHSP+DL E +LD E+KSW AFA+Q
Sbjct: 303 RNVWRCELEQVLAQLQPAQERFGDNLWVSSSCSLLHSPVDLDREDKLDPELKSWLAFAVQ 362
Query: 352 KCHELALLRDALNSGDT----AALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRA 407
KC E+A+LRDALN + ALAE +R S R+H V+ R+ AI A DSQR
Sbjct: 363 KCGEIAVLRDALNDPQSPKVQTALAESRTIAASRAQSPRIHKADVQARINAIGAADSQRL 422
Query: 408 NVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQ 467
+ + R Q+AR KLPA+PTTTIGSFPQT IR R FK+G L AN+Y + I+
Sbjct: 423 SPFTKRIAQQQARLKLPAFPTTTIGSFPQTASIRLARQAFKQGKLSANDYTDAMHSEIRH 482
Query: 468 AIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDIS 527
A+ QERLGLDVLVHGEAERNDMVEYF E LDG++FT+ GWVQSYGSRCVKP I+ GD+S
Sbjct: 483 AVQIQERLGLDVLVHGEAERNDMVEYFAEQLDGYLFTRFGWVQSYGSRCVKPAIIYGDLS 542
Query: 528 RPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVAD 587
RP P+TV+W YAQSLTDK +KGMLTGPVT+L WSFPREDVSR+ A+Q+ALALRDEV D
Sbjct: 543 RPKPMTVDWITYAQSLTDKVMKGMLTGPVTMLMWSFPREDVSRKIQAQQLALALRDEVVD 602
Query: 588 LEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEF 647
LE AGI I+QIDE A REGLPLRR+ W YL W VEAFR++A+ +D+TQIHTHMCY EF
Sbjct: 603 LENAGIKIVQIDEAAFREGLPLRRAQWQEYLDWAVEAFRLSASGVRDETQIHTHMCYSEF 662
Query: 648 NDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEAL 707
ND+++SIAA+DADVITIETSRSDMELLE+FE FDYPN+IGPGVYDIHSP VP + L
Sbjct: 663 NDVIESIAAMDADVITIETSRSDMELLEAFEAFDYPNDIGPGVYDIHSPRVPDTVEMVKL 722
Query: 708 LKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
+ KA KRIPAERLWVNPDCGLKTR WPET AAL NMV AA+ LR
Sbjct: 723 MSKAVKRIPAERLWVNPDCGLKTRAWPETEAALVNMVAAARQLR 766
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: 1744
Number of extensions: 81
Number of successful extensions: 7
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: 770
Length adjustment: 40
Effective length of query: 713
Effective length of database: 730
Effective search space: 520490
Effective search space used: 520490
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 Pf1N1B4_783 (5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14))
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.8131.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 1115.0 0.0 0 1114.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 5-methyltetrahydropteroyltriglut
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1114.8 0.0 0 0 1 754 [] 7 768 .. 7 768 .. 0.98
Alignments for each domain:
== domain 1 score: 1114.8 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLd 65
lgfPrig+ Relkkale+ywkg++++++l++v ++lr+++++ qk+ag+d++pv+df++YD+vL+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 7 LGFPRIGADRELKKALEAYWKGDLDQDALKSVGRHLRATHWQLQKDAGIDLLPVGDFAWYDQVLT 71
79*************************************************************** PP
TIGR01371 66 tavllgaiperfkeladde..sdldtyFaiaRGtek........kdvaalemtkwfntnYhYlvP 120
++ +g+iperf++ +d++ +ldt+Fa+aRG + + a+e+tkwf+tnYhYlvP
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 72 HSLTFGVIPERFDSAKDERglPTLDTLFAMARGATAaccggehtQAQYAQELTKWFDTNYHYLVP 136
*************9876652246**********9889***99987789***************** PP
TIGR01371 121 elskeeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYk 185
e++++++fkls+++l++e++eak+lg+++kPv++Gp+t+l+L+kak ++++++l+lle+llp+Y
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 137 EFTADQQFKLSWEQLFDEVDEAKALGHNVKPVIIGPLTYLWLGKAK-GNDFDKLDLLERLLPIYG 200
*********************************************9.589*************** PP
TIGR01371 186 evlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealekl 250
e+l +la++gvewvqideP+l ldl++++++a+++ay+ l+ + lk l++tYf +e++l +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 201 EILGRLAAQGVEWVQIDEPILTLDLPQAWKNAFERAYHILQY--SPLKKLVATYFSGLEDNLGLA 263
****************************************96..6778899************** PP
TIGR01371 251 vslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdkl 315
vslpv++l++D v+a+++l ++ ++++ k+L++G+++Grn+w+ +le++l++l+ +++ gd+l
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 264 VSLPVQGLHIDAVRAPDQLGQVLDRLPTYKILSVGLVNGRNVWRCELEQVLAQLQPAQERFGDNL 328
***************************************************************** PP
TIGR01371 316 vvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg..eaavaealeaeaaai 378
+vs+scsllh+pvdl++e+kld+elk++lafa++k+ e++vl++al++ + +v++al+++++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 329 WVSSSCSLLHSPVDLDREDKLDPELKSWLAFAVQKCGEIAVLRDALNDpqSPKVQTALAESRTIA 393
************************************************84445667777777778 PP
TIGR01371 379 aarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRka 443
a+r++s+r+++++v++r++a+ +++++r s+f++R ++q+++l+lP++PtttiGsfPqt+++R a
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 394 ASRAQSPRIHKADVQARINAIGAADSQRLSPFTKRIAQQQARLKLPAFPTTTIGSFPQTASIRLA 458
899************************************************************** PP
TIGR01371 444 RakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngW 508
R++f++g++s+++Y++++++ei++++++qe+lglDvLvhGe+eRnDmveyF+e+l+G++ft++gW
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 459 RQAFKQGKLSANDYTDAMHSEIRHAVQIQERLGLDVLVHGEAERNDMVEYFAEQLDGYLFTRFGW 523
***************************************************************** PP
TIGR01371 509 vqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkei 573
vqsYGsRcvkP+iiygd+srpkpmtv++++yaqslt+k +kGmLtGPvt+l Wsf+ReD++rk +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 524 VQSYGSRCVKPAIIYGDLSRPKPMTVDWITYAQSLTDKVMKGMLTGPVTMLMWSFPREDVSRKIQ 588
***************************************************************** PP
TIGR01371 574 aeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqi 638
a+q+alalrdev+dLe+agiki+qiDe+a+ReglPlr+++++eYldwaveaFrl+asgv+detqi
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 589 AQQLALALRDEVVDLENAGIKIVQIDEAAFREGLPLRRAQWQEYLDWAVEAFRLSASGVRDETQI 653
***************************************************************** PP
TIGR01371 639 hthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPske 703
hthmCYsefn++ie+iaa+daDvi+ie+srsdmell+a+++ ++y+++iG+GvyDihsprvP +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 654 HTHMCYSEFNDVIESIAAMDADVITIETSRSDMELLEAFEA-FDYPNDIGPGVYDIHSPRVPDTV 717
*****************************************.77********************* PP
TIGR01371 704 elaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
e+ +l++ka+k++p+erlWvnPDCGLktR+w+e++aal n+v+aa++lR++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_783 718 EMVKLMSKAVKRIPAERLWVNPDCGLKTRAWPETEAALVNMVAAARQLRSQ 768
*************************************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (770 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: 11.77
//
[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