Align 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 3, chloroplastic; Cobalamin-independent methionine synthase 3; AtMS3; EC 2.1.1.14 (characterized)
to candidate WP_041667267.1 SULKU_RS13655 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= SwissProt::Q0WNZ5
(812 letters)
>NCBI__GCF_000183725.1:WP_041667267.1
Length = 741
Score = 680 bits (1755), Expect = 0.0
Identities = 372/758 (49%), Positives = 501/758 (66%), Gaps = 25/758 (3%)
Query: 53 IVGYPRIGPKRELKFALESFWDGKTNVDDLQNVAANLRKSIWKHMAHAGIKYIPSNTFSY 112
++G+PRIG KRELKFALESFW G D+L+ +A++LRK W +GI+ + N FS+
Sbjct: 8 LLGFPRIGEKRELKFALESFWKGTIGFDELETIASDLRKRHWNLQRDSGIQKVAINDFSF 67
Query: 113 YDQMLDTTAMLGAVPSRYGWESGEIGFDVYFSMARGNASAHAMEMTKWFDTNYHYIVPEL 172
YD MLD LGA P R+ S I YF+MARG+ S AMEMTKWF+TNYHY+VPEL
Sbjct: 68 YDTMLDIMVTLGATPERFSDISDPIRR--YFTMARGDESHVAMEMTKWFNTNYHYLVPEL 125
Query: 173 GPDVNFSYASHKAVV-EFKEAKALGIDTVPVLIGPMTYLLLSKPAKGVEKSFCLLSLIDK 231
F + + ++ EF EAKALG++ LIGPMT+ LSK ++ V ++ L DK
Sbjct: 126 HDQFVFGAVNAEKIIHEFNEAKALGLEGCIQLIGPMTFFALSKCSESVRQA-----LFDK 180
Query: 232 ILPVYKEVLADLKSAGARWIQFDEPILVMDLDTSQLQAFSDAYSHMESSLAGLNVLIATY 291
++ Y +L L++ A I EP LV D L AY + +LA L +ATY
Sbjct: 181 VIAQYVALLETLQALDAEII-IHEPSLVCDPTPHDLSLLKIAYDRL-GTLAPL--WVATY 236
Query: 292 FADVPAEAYKTLMSLKCVTGFGFDLVRGLETLDLIKMNFPRGKLLFAGVVDGRNIWANDL 351
F + EA L+ + G D V G + ++ +++ K + G+++GRN+W NDL
Sbjct: 237 F-EHSNEATAVLVHTP-IKGLYLDFVHGEKNIESLEVLGKSDKHVSVGIINGRNVWKNDL 294
Query: 352 SASLKTLQTLEDIVGKEKVVVSTSCSLLHTAVDLVNEMKLDKELKSWLAFAAQKVVEVNA 411
SASLKTL T+ D + KE++ +S+SCSLLH L +E LD +K+ LAFA +K+ E++A
Sbjct: 295 SASLKTLNTIADYIPKERLSLSSSCSLLHVPYTLRHETTLDANVKTLLAFAEEKLTELSA 354
Query: 412 LAKSFSGAKDEALFSSNSMRQASRRSSPRVTNAAVQQDVDAVKKSDHHRSTEVSVRLQAQ 471
L+K+F +E ++ +R P T+ AVQ + A++ D+ R+ +R +A
Sbjct: 355 LSKAFFD-NEEIVY---------QRYDPSRTDPAVQIRLSALQSGDYKRTYPFPLRQEAA 404
Query: 472 QKKLNLPALPTTTIGSFPQTTDLRRIRREFKAKKISEVDYVQTIKEEYEKVIKLQEELGI 531
+LP LPTTTIGSFPQT D+R+IR+EFK IS Y +K ++ QE + +
Sbjct: 405 HDLFDLPILPTTTIGSFPQTADIRKIRQEFKKGLISREIYEIEMKNGIRDCVEFQESIDL 464
Query: 532 DVLVHGEAERNDMVEFFGEQLSGFAFTSNGWVQSYGSRCVKPPIIYGDITRPKAMTVFWS 591
DVLVHGE ERNDMVE+FGEQLSGFAF+SNGWVQSYGSRCVKPP++YGD++RP MT+ WS
Sbjct: 465 DVLVHGEFERNDMVEYFGEQLSGFAFSSNGWVQSYGSRCVKPPLLYGDVSRPYPMTLEWS 524
Query: 592 SMAQKMTQRPMKGMLTGPVTILNWSFVRNDQPRHETCFQIALAIKDEVEDLEKAGVTVIQ 651
AQ +T R MKGMLTGPVTILNWSFVR+DQPR T QIALAI+DEV+DL+++G+ +IQ
Sbjct: 525 LFAQSLTARSMKGMLTGPVTILNWSFVRDDQPRSLTSTQIALAIRDEVDDLQRSGIKMIQ 584
Query: 652 IDEAALREGLPLRKSEQKFYLDWAVHAFRITNSGVQDSTQIHTHMCYSNFNDIIHSIIDM 711
+DEAA +EG PLR+ ++ Y WA+ +F ++ + + TQIHTHMCYS F DII +I M
Sbjct: 585 VDEAAFKEGYPLRREKRAEYEKWALESFLLSTAVAERDTQIHTHMCYSEFTDIIKTIEAM 644
Query: 712 DADVITIENSRSDEKLLSVFHEGVKYGAGIGPGVYDIHSPRIPSTEEIAERINKMLAVLD 771
DADVI+IE SRS +LL +F E V Y +G GVYDIHSPRIPS EE+ ++I+ +L VL
Sbjct: 645 DADVISIETSRSGNRLLKIFAE-VGYAQEVGLGVYDIHSPRIPSIEEMEKQIHALLEVLP 703
Query: 772 SKVLWVNPDCGLKTRNYSEVKSALSNMVAAAKLIRSQL 809
+ LW+NPDCGLKTR ++E K+AL NMV A K +R L
Sbjct: 704 AAQLWINPDCGLKTRGWAETKAALENMVEATKRVRQSL 741
Lambda K H
0.318 0.133 0.387
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: 1294
Number of extensions: 52
Number of successful extensions: 6
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: 812
Length of database: 741
Length adjustment: 41
Effective length of query: 771
Effective length of database: 700
Effective search space: 539700
Effective search space used: 539700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)
Align candidate WP_041667267.1 SULKU_RS13655 (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.32439.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.3e-296 970.8 0.0 4.9e-296 970.6 0.0 1.0 1 lcl|NCBI__GCF_000183725.1:WP_041667267.1 SULKU_RS13655 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_041667267.1 SULKU_RS13655 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 970.6 0.0 4.9e-296 4.9e-296 1 753 [. 9 739 .. 9 740 .. 0.97
Alignments for each domain:
== domain 1 score: 970.6 bits; conditional E-value: 4.9e-296
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrigekRelk+ale++wkg+i +el++ a+dlrk++++ q+++g++ +++ndfs+YD++Ld+ v
lcl|NCBI__GCF_000183725.1:WP_041667267.1 9 LGFPRIGEKRELKFALESFWKGTIGFDELETIASDLRKRHWNLQRDSGIQKVAINDFSFYDTMLDIMVT 77
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeef.klsknklle 137
lga perf++++ d + +yF++aRG+e+ ++a+emtkwfntnYhYlvPel+++ f +++++k+++
lcl|NCBI__GCF_000183725.1:WP_041667267.1 78 LGATPERFSDIS-D--PIRRYFTMARGDES--HVAMEMTKWFNTNYHYLVPELHDQFVFgAVNAEKIIH 141
**********93.3..489********966..9***********************99966899***** PP
TIGR01371 138 eykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvl 206
e++eak+lg+e l+Gp+tf+ L+k +e + +++l +k++ Y +l++l++ ++e i eP l
lcl|NCBI__GCF_000183725.1:WP_041667267.1 142 EFNEAKALGLEGCIQLIGPMTFFALSKCSE---SVRQALFDKVIAQYVALLETLQALDAEI-IIHEPSL 206
***************************996...568999*****************99875.59***** PP
TIGR01371 207 vldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakak 275
v+d ++++l+++k ay+ l + l ++tYf++ +ea + lv++p+++l lD+v+++++ e ++
lcl|NCBI__GCF_000183725.1:WP_041667267.1 207 VCDPTPHDLSLLKIAYDRLGT---LAPLWVATYFEHSNEATAVLVHTPIKGLYLDFVHGEKNIESLEVL 272
*******************97...799***********************************9999999 PP
TIGR01371 276 feedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvpvdleleekldkelkel 343
++dk +++G+i+Grn+wk+dl++slk+l++++++ ++l +s+scsllhvp++l++e++ld+++k+l
lcl|NCBI__GCF_000183725.1:WP_041667267.1 273 GKSDKHVSVGIINGRNVWKNDLSASLKTLNTIADYIPkERLSLSSSCSLLHVPYTLRHETTLDANVKTL 341
9********************************998779****************************** PP
TIGR01371 344 lafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfee 412
lafa+ekl+el++l++a+ +++ +i ++ ++ ++d +v+ rl+al++ + +r+ +f
lcl|NCBI__GCF_000183725.1:WP_041667267.1 342 LAFAEEKLTELSALSKAFFDNE-----------EIVYQRYDPSRTDPAVQIRLSALQSGDYKRTYPFPL 399
****************999722...........23344567788999********************** PP
TIGR01371 413 RaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLv 481
R+ea ++ ++lP+lPtttiGsfPqt+++Rk R++f+kg is+e Ye +k+ i++++++qe+++lDvLv
lcl|NCBI__GCF_000183725.1:WP_041667267.1 400 RQEAAHDLFDLPILPTTTIGSFPQTADIRKIRQEFKKGLISREIYEIEMKNGIRDCVEFQESIDLDVLV 468
********************************************************************* PP
TIGR01371 482 hGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkG 550
hGefeRnDmveyFge+l+Gfaf +ngWvqsYGsRcvkPp++ygdvsrp pmt+++s +aqslt + +kG
lcl|NCBI__GCF_000183725.1:WP_041667267.1 469 HGEFERNDMVEYFGEQLSGFAFSSNGWVQSYGSRCVKPPLLYGDVSRPYPMTLEWSLFAQSLTARSMKG 537
********************************************************************* PP
TIGR01371 551 mLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYld 619
mLtGPvtilnWsfvR+D+pr+ +++qiala+rdev dL+ +gik+iq+De+a++eg Plr+++++eY +
lcl|NCBI__GCF_000183725.1:WP_041667267.1 538 MLTGPVTILNWSFVRDDQPRSLTSTQIALAIRDEVDDLQRSGIKMIQVDEAAFKEGYPLRREKRAEYEK 606
********************************************************************* PP
TIGR01371 620 waveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiG 688
wa+e+F l+++ ++ +tqihthmCYsef +ii++i+a+daDvisie+srs ll+ + e ++y++e+G
lcl|NCBI__GCF_000183725.1:WP_041667267.1 607 WALESFLLSTAVAERDTQIHTHMCYSEFTDIIKTIEAMDADVISIETSRSGNRLLKIFAE-VGYAQEVG 674
************************************************************.88****** PP
TIGR01371 689 lGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
lGvyDihspr+Ps ee+++++++ l++lp+ +lW+nPDCGLktR w e+kaal+n+vea+k++R+
lcl|NCBI__GCF_000183725.1:WP_041667267.1 675 LGVYDIHSPRIPSIEEMEKQIHALLEVLPAAQLWINPDCGLKTRGWAETKAALENMVEATKRVRQ 739
***************************************************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (741 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: 12.88
//
[ok]
This GapMind analysis is from Apr 10 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