Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate Pf6N2E2_5472 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472
Length = 770
Score = 946 bits (2444), Expect = 0.0
Identities = 477/764 (62%), Positives = 569/764 (74%), Gaps = 16/764 (2%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
L HTLGFPR+G RELKKA E+YW G+ L AVGRELRARHW QK AGIDLLPVGD
Sbjct: 3 LAHTLGFPRIGADRELKKALEAYWKGDLAPAALQAVGRELRARHWQLQKDAGIDLLPVGD 62
Query: 64 FAWYDHVLTTSLLLGNVPARHQ---NKDGSVDIDTLFRIGRGR------APTGEPAAAAE 114
FAWYD VL+ SL LG VP R N G +DTLF + RG A G+ A E
Sbjct: 63 FAWYDQVLSHSLTLGVVPPRFHSTLNAQGRPTLDTLFAMARGATASCCGADHGQAQYAQE 122
Query: 115 MTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVK 174
+TKWF+TNYHY+VPEF Q F L+W QL DEVDEA ALGH+VKPV++GP+T+LWLGK K
Sbjct: 123 LTKWFDTNYHYLVPEFSADQTFALSWEQLFDEVDEAHALGHQVKPVIIGPLTYLWLGKAK 182
Query: 175 GEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ- 233
GE FD+L LL +LPVY ++L L +G+EWVQIDEP L L+LPQAW A++ AY LQ
Sbjct: 183 GEAFDKLGLLERLLPVYGEILNRLKAQGVEWVQIDEPILTLDLPQAWKSAFERAYHILQY 242
Query: 234 GQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLING 293
+K L+ TYF G+ NL +LPV GLH+D V + + ++ RLP+ +LS GL+NG
Sbjct: 243 SPLKKLVATYFSGLQDNLGLAVSLPVDGLHIDAVRAPEQLGQVLDRLPTYKILSVGLVNG 302
Query: 294 RNVWRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQ 351
RNVWR +L + AQ++ + +LWV++SCSLLHSP+DL E RLD E+KSW AFA+Q
Sbjct: 303 RNVWRCELEQALAQLQPAQERFGDNLWVSTSCSLLHSPVDLEREDRLDPELKSWLAFAVQ 362
Query: 352 KCHELALLRDALNSGDTAALAEW---SAPIQARR-HSTRVHNPAVEKRLAAITAQDSQRA 407
KC E+A+LRDALN A+ + S +QA R S R+H PAV+ RLAAI QDSQR
Sbjct: 363 KCGEVAVLRDALNDPHAPAVQQALADSREVQASRARSARIHKPAVQARLAAIGPQDSQRR 422
Query: 408 NVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQ 467
+ + R E QRAR KLPA+PTTTIGSFPQT IR R +K+G L AN+Y+ + I+
Sbjct: 423 SPFAKRIERQRARLKLPAFPTTTIGSFPQTPAIRLARQAYKQGKLSANDYQDAMHTEIRH 482
Query: 468 AIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDIS 527
A+ QERLGLDVLVHGEAERNDMVEYF EHLDG+VFT+ GWVQSYGSRCVKP I+ GDIS
Sbjct: 483 AVQIQERLGLDVLVHGEAERNDMVEYFAEHLDGYVFTRFGWVQSYGSRCVKPAIIYGDIS 542
Query: 528 RPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVAD 587
RP+ +TV+W +YAQSLTDK +KGMLTGPVT+L WSFPREDVSR+ A+Q+ALALRDEV D
Sbjct: 543 RPSAMTVDWIRYAQSLTDKVMKGMLTGPVTMLMWSFPREDVSRQVQARQLALALRDEVLD 602
Query: 588 LEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEF 647
LE AGI I+QIDE A REGLPLRR W YL W V+AFR+ A+ D+TQIHTHMCY EF
Sbjct: 603 LEKAGIKIVQIDEAAFREGLPLRRGQWQEYLDWAVDAFRLCASGVADETQIHTHMCYSEF 662
Query: 648 NDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEAL 707
ND++ +IA +DADVITIETSRSDMELLE+FE FDYPN+IGPGVYDIHSP VP + AL
Sbjct: 663 NDVIKAIADMDADVITIETSRSDMELLEAFEAFDYPNDIGPGVYDIHSPRVPDTAEMVAL 722
Query: 708 LKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
+ KA KRI AERLW+NPDCGLKTRGWPET AAL NMV AA+ LR
Sbjct: 723 MSKAVKRIAAERLWINPDCGLKTRGWPETEAALVNMVAAARQLR 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: 1749
Number of extensions: 68
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: 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 Pf6N2E2_5472 (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.21630.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 1094.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 5-methyltetrahydropteroyltriglut
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1094.7 0.0 0 0 1 754 [] 7 768 .. 7 768 .. 0.97
Alignments for each domain:
== domain 1 score: 1094.7 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvL 64
lgfPrig+ Relkkale+ywkg++ ++l++v ++lr+++++ qk+ag+d++pv+df++YD+vL
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 7 LGFPRIGADRELKKALEAYWKGDLAPAALQAVGRELRARHWQLQKDAGIDLLPVGDFAWYDQVL 70
79************************************************************** PP
TIGR01371 65 dtavllgaiperfkel..addesdldtyFaiaRGtek........kdvaalemtkwfntnYhYl 118
++ lg++p rf+++ a+++ +ldt+Fa+aRG + + a+e+tkwf+tnYhYl
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 71 SHSLTLGVVPPRFHSTlnAQGRPTLDTLFAMARGATAsccgadhgQAQYAQELTKWFDTNYHYL 134
*************98722344567**********9889****9988889*************** PP
TIGR01371 119 vPelskeeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllp 182
vPe+s++++f+ls+++l++e++ea++lg+++kPv++Gp+t+l+L+kak +e +++l lle+llp
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 135 VPEFSADQTFALSWEQLFDEVDEAHALGHQVKPVIIGPLTYLWLGKAK-GEAFDKLGLLERLLP 197
***********************************************9.588************ PP
TIGR01371 183 vYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveea 246
vY e+l++l+++gvewvqideP+l ldl++++++a+++ay+ l+ + lk l++tYf ++++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 198 VYGEILNRLKAQGVEWVQIDEPILTLDLPQAWKSAFERAYHILQY--SPLKKLVATYFSGLQDN 259
*******************************************96..6778899********** PP
TIGR01371 247 leklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleak 310
l +vslpv++l++D v+a+e+l ++ ++++ k+L++G+++Grn+w+ +le++l++l+ +++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 260 LGLAVSLPVDGLHIDAVRAPEQLGQVLDRLPTYKILSVGLVNGRNVWRCELEQALAQLQPAQER 323
**************************************************************** PP
TIGR01371 311 agdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.ea.avaeale 372
gd+l+vstscsllh+pvdle+e++ld+elk++lafa++k+ e++vl++al++ +a av++al+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 324 FGDNLWVSTSCSLLHSPVDLEREDRLDPELKSWLAFAVQKCGEVAVLRDALNDpHApAVQQALA 387
*****************************************************96515566667 PP
TIGR01371 373 aeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPq 436
++++ a+r++s+r+++ +v++rl+a+ ++++r+s+f++R e q+++l+lP++PtttiGsfPq
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 388 DSREVQASRARSARIHKPAVQARLAAIGPQDSQRRSPFAKRIERQRARLKLPAFPTTTIGSFPQ 451
77777788999***************************************************** PP
TIGR01371 437 tkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaG 500
t +R aR+++++g++s+++Y++++++ei++++++qe+lglDvLvhGe+eRnDmveyF+e+l+G
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 452 TPAIRLARQAYKQGKLSANDYQDAMHTEIRHAVQIQERLGLDVLVHGEAERNDMVEYFAEHLDG 515
**************************************************************** PP
TIGR01371 501 faftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfv 564
++ft++gWvqsYGsRcvkP+iiygd+srp +mtv++++yaqslt+k +kGmLtGPvt+l Wsf+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 516 YVFTRFGWVQSYGSRCVKPAIIYGDISRPSAMTVDWIRYAQSLTDKVMKGMLTGPVTMLMWSFP 579
**************************************************************** PP
TIGR01371 565 ReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrla 628
ReD++r+ +a+q+alalrdev dLe+agiki+qiDe+a+ReglPlr+ +++eYldwav+aFrl
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 580 REDVSRQVQARQLALALRDEVLDLEKAGIKIVQIDEAAFREGLPLRRGQWQEYLDWAVDAFRLC 643
**************************************************************** PP
TIGR01371 629 asgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvy 692
asgv+detqihthmCYsefn++i+aia++daDvi+ie+srsdmell+a+++ ++y+++iG+Gvy
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 644 ASGVADETQIHTHMCYSEFNDVIKAIADMDADVITIETSRSDMELLEAFEA-FDYPNDIGPGVY 706
***************************************************.77********** PP
TIGR01371 693 DihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
DihsprvP + e+ +l++ka+k++++erlW+nPDCGLktR w+e++aal n+v+aa++lR++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5472 707 DIHSPRVPDTAEMVALMSKAVKRIAAERLWINPDCGLKTRGWPETEAALVNMVAAARQLRSQ 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 8.06
//
[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