Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate PfGW456L13_3767 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767
Length = 762
Score = 917 bits (2371), Expect = 0.0
Identities = 457/756 (60%), Positives = 562/756 (74%), Gaps = 10/756 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H+LGFPR+G RELKKAQE++W G L VGR+LR HWD QK+AGI+LLPVGDFA
Sbjct: 5 HSLGFPRIGRDRELKKAQEAFWKGELDEAGLRTVGRDLRKTHWDLQKKAGIELLPVGDFA 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAA-AAEMTKWFNTNYH 124
WYD VLT SL+ G +P R + DG + TLF + RG + + A A EMTKWF+TNYH
Sbjct: 65 WYDQVLTHSLMFGVIPERFRPHDGKASLQTLFGMARGVSDSCCGGAHAQEMTKWFDTNYH 124
Query: 125 YMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLL 184
Y+VPEF QQF+L W QL +EV+EA ALGH VKPV++GP+T+LWLGK KG +FD+L LL
Sbjct: 125 YLVPEFSADQQFQLGWDQLFEEVEEARALGHNVKPVIIGPLTYLWLGKAKGVEFDKLELL 184
Query: 185 NDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQ-VKLLLTTY 243
+ +LP+Y Q+ LA +G+EWVQIDEP LVL+LPQ W +A++ AY+ +Q +K L+ TY
Sbjct: 185 DRLLPLYGQIFQRLAAQGVEWVQIDEPILVLDLPQDWKNAFERAYNLIQRDPLKKLVATY 244
Query: 244 FEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTE 303
F G+ NL LPV GLH+DLV + + RLP+ +LS GL+NGRNVWR DL
Sbjct: 245 FGGLEENLGLAANLPVDGLHIDLVRAPEQYPTILDRLPAYKVLSLGLVNGRNVWRCDLEN 304
Query: 304 KYAQIK---DIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLR 360
A ++ + +G R LWVA SCSLLHSP+DL E +LDAE+KSW AFA+QKC E+A+L
Sbjct: 305 ALATLQHAHERLGDR-LWVAPSCSLLHSPVDLGREDKLDAELKSWLAFAVQKCEEVAVLA 363
Query: 361 DALNSGDTAALAE---WSAPIQARRH-STRVHNPAVEKRLAAITAQDSQRANVYEVRAEA 416
A+N + + E S +QA R S R+H PAV+ R+AAIT +DSQR +++ R E
Sbjct: 364 QAVNEPEAPKVLEALTQSRAVQASRAASPRIHKPAVQARVAAITVKDSQRHSLFARRIEK 423
Query: 417 QRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLG 476
QRA LP +PTTTIGSFPQT IR R +K+G L Y + I+ A+ QE LG
Sbjct: 424 QRAGLNLPLFPTTTIGSFPQTASIRLARQSYKQGKLTEAEYTEAMHSEIRHAVQVQENLG 483
Query: 477 LDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEW 536
LDVLVHGEAERNDMVEYF E LDG+VFT+ GWVQSYGSRCVKP ++ GD+SRP +TVEW
Sbjct: 484 LDVLVHGEAERNDMVEYFAEQLDGYVFTRFGWVQSYGSRCVKPAVIFGDLSRPKAMTVEW 543
Query: 537 AKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGII 596
+YAQ LTDK +KGMLTGPVT+L WSFPREDV+RE A+Q+ALA+RDEV DLEAAGI I+
Sbjct: 544 IRYAQGLTDKVMKGMLTGPVTMLMWSFPREDVTREVQARQLALAIRDEVVDLEAAGIKIV 603
Query: 597 QIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAA 656
QIDE A REGLPLR++ W YL W E FR+ A+ +D+TQIHTHMCY EFND+++SIAA
Sbjct: 604 QIDEAAFREGLPLRQAQWQHYLDWATEVFRLCASGVRDETQIHTHMCYSEFNDVIESIAA 663
Query: 657 LDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIP 716
+DADVITIETSRSDMELL++FE F YPNEIGPGVYDIHSP VP + LL+KAAKRIP
Sbjct: 664 MDADVITIETSRSDMELLDAFEAFAYPNEIGPGVYDIHSPRVPDSSEMANLLRKAAKRIP 723
Query: 717 AERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
A+RLWVNPDCGLKTRGWPET AAL +MV AA+ LR+
Sbjct: 724 ADRLWVNPDCGLKTRGWPETEAALVHMVNAARQLRK 759
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: 1720
Number of extensions: 70
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: 762
Length adjustment: 40
Effective length of query: 713
Effective length of database: 722
Effective search space: 514786
Effective search space used: 514786
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 PfGW456L13_3767 (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.22630.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 1107.1 0.0 0 1107.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 5-methyltetrahydropteroyltriglut
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltr
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1107.0 0.0 0 0 1 754 [] 7 760 .. 7 760 .. 0.98
Alignments for each domain:
== domain 1 score: 1107.0 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvn 55
lgfPrig+ Relkka+e++wkg+++++ l +v +dlrk++++ qk+ag++++pv+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 7 LGFPRIGRDRELKKAQEAFWKGELDEAGLRTVGRDLRKTHWDLQKKAGIELLPVG 61
79***************************************************** PP
TIGR01371 56 dfslYDhvLdtavllgaiperfkeladdesdldtyFaiaRGtek...kdvaalem 107
df++YD+vL+ ++++g+iperf+ d++++l+t+F +aRG ++ +++a+em
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 62 DFAWYDQVLTHSLMFGVIPERFRPH-DGKASLQTLFGMARGVSDsccGGAHAQEM 115
************************8.66679**********988888899***** PP
TIGR01371 108 tkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvllGpitflkL 162
tkwf+tnYhYlvPe+s++++f+l +++l+ee++ea++lg+++kPv++Gp+t+l+L
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 116 TKWFDTNYHYLVPEFSADQQFQLGWDQLFEEVEEARALGHNVKPVIIGPLTYLWL 170
******************************************************* PP
TIGR01371 163 akakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaa 217
+kak + e+++lell++llp+Y +++++la++gvewvqideP+lvldl++++++a
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 171 GKAK-GVEFDKLELLDRLLPLYGQIFQRLAAQGVEWVQIDEPILVLDLPQDWKNA 224
**99.589*********************************************** PP
TIGR01371 218 vkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelela 272
+++ay+ +++ lk l++tYf+ +ee+l +++lpv++l++Dlv+a+e+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 225 FERAYNLIQR--DPLKKLVATYFGGLEENLGLAANLPVDGLHIDLVRAPEQYPTI 277
*******997..5778899************************************ PP
TIGR01371 273 kakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvp 327
++++ kvL++G+++Grn+w+ dle++l++l++ +++ gd+l+v++scsllh+p
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 278 LDRLPAYKVLSLGLVNGRNVWRCDLENALATLQHAHERLGDRLWVAPSCSLLHSP 332
******************************************************* PP
TIGR01371 328 vdleleekldkelkellafakekleelkvlkealeg..eaavaealeaeaaaiaa 380
vdl +e+kld+elk++lafa++k+ee++vl++a+++ +v eal++++a a+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 333 VDLGREDKLDAELKSWLAFAVQKCEEVAVLAQAVNEpeAPKVLEALTQSRAVQAS 387
***********************************98444667788888888889 PP
TIGR01371 381 rkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfP 435
r+ s+r+++ +v++r++a++ k+++r+s f++R e+q++ lnlPl+PtttiGsfP
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 388 RAASPRIHKPAVQARVAAITVKDSQRHSLFARRIEKQRAGLNLPLFPTTTIGSFP 442
99***************************************************** PP
TIGR01371 436 qtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDm 490
qt+++R aR+++++g+++e+eY++++++ei++++++qe+lglDvLvhGe+eRnDm
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 443 QTASIRLARQSYKQGKLTEAEYTEAMHSEIRHAVQVQENLGLDVLVHGEAERNDM 497
******************************************************* PP
TIGR01371 491 veyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqslts 545
veyF+e+l+G++ft++gWvqsYGsRcvkP++i+gd+srpk+mtv++++yaq+lt+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 498 VEYFAEQLDGYVFTRFGWVQSYGSRCVKPAVIFGDLSRPKAMTVEWIRYAQGLTD 552
******************************************************* PP
TIGR01371 546 kpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDe 600
k +kGmLtGPvt+l Wsf+ReD+ r+ +a+q+ala+rdev+dLe+agiki+qiDe
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 553 KVMKGMLTGPVTMLMWSFPREDVTREVQARQLALAIRDEVVDLEAAGIKIVQIDE 607
******************************************************* PP
TIGR01371 601 palReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaia 655
+a+ReglPlr++++++Yldwa e+Frl asgv+detqihthmCYsefn++ie+ia
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 608 AAFREGLPLRQAQWQHYLDWATEVFRLCASGVRDETQIHTHMCYSEFNDVIESIA 662
******************************************************* PP
TIGR01371 656 aldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaelle 710
a+daDvi+ie+srsdmellda+++ ++y++eiG+GvyDihsprvP + e+a+ll+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 663 AMDADVITIETSRSDMELLDAFEA-FAYPNEIGPGVYDIHSPRVPDSSEMANLLR 716
************************.67**************************** PP
TIGR01371 711 kalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
ka k++p++rlWvnPDCGLktR w+e++aal ++v+aa++lR++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 717 KAAKRIPADRLWVNPDCGLKTRGWPETEAALVHMVNAARQLRKE 760
*****************************************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (762 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: 11.94
//
[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