Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate AZOBR_RS24275 AZOBR_RS24275 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__azobra:AZOBR_RS24275
Length = 772
Score = 852 bits (2200), Expect = 0.0
Identities = 446/769 (57%), Positives = 551/769 (71%), Gaps = 28/769 (3%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
HTLGFPR+G +RELK A E+YW G S+R+EL+ VG +LR RHW + Q +DL+PVGDFA
Sbjct: 5 HTLGFPRIGAKRELKFALEAYWKGASSRDELVRVGADLRKRHW--RDQGALDLVPVGDFA 62
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGR-----APTGEP-------AAAA 113
+YD VL S LGN+P R + G +D FR+ RGR A + E AA
Sbjct: 63 FYDQVLDMSFTLGNLPERVKGFHGDA-LDNYFRVARGRSAETAAHSAEEHGGCCGGVAAG 121
Query: 114 EMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKV 173
EMTKWF+TNYHY+VPEF G F L ++LL+++ EA A G K KPV++GPVT+L LGK
Sbjct: 122 EMTKWFDTNYHYIVPEFDAGTTFTLDASRLLEQLAEAKAQGVKAKPVIVGPVTYLALGKA 181
Query: 174 KGEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDAL- 232
K + D+L+LL +LPVY +L L +G+EWVQIDEP LV EL AW DA+ AY AL
Sbjct: 182 K-DGSDKLALLPRLLPVYAGLLQALTDQGVEWVQIDEPILVTELEAAWRDAFTQAYRALG 240
Query: 233 QGQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLIN 292
G VKLLL TYF + NL +LPVQGLH+D + +D+V L + LP+D ++S G++N
Sbjct: 241 TGAVKLLLATYFGQLQDNLPLACSLPVQGLHLDAITARDEVDALIQALPTDRVVSLGVVN 300
Query: 293 GRNVWRADLTEKYAQIKDI---VGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFA 349
GRN+W+ DL ++ + +G+R LW+A SCSLLH P+DL+ E +LD E +SW AFA
Sbjct: 301 GRNIWKTDLGATLDWLEPVAERLGER-LWIAPSCSLLHVPVDLAGERKLDEEARSWLAFA 359
Query: 350 LQKCHELALLRDAL----NSGDTAALAEWSA---PIQARRHSTRVHNPAVEKRLAAITAQ 402
+QK E+ +L AL + G A AE A ++ARRHS RV+NPAV+ +AAI A+
Sbjct: 360 VQKLEEIRVLAIALTPGRDGGRAAVAAELDANRAAVEARRHSPRVNNPAVKAAVAAIDAR 419
Query: 403 DSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIA 462
+R + + RA Q R LP +PTTTIGSFPQT EIR R FK G +DA Y +
Sbjct: 420 LGRRKSAFIERAAKQATRLNLPKFPTTTIGSFPQTKEIRQARSQFKAGTIDAVAYTEAMR 479
Query: 463 EHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIV 522
I +++ EQE LGLDVLVHGEAERNDMVEYFGE LDG+VF+Q GWVQSYGSRCVKPPI+
Sbjct: 480 GEIARSVREQEALGLDVLVHGEAERNDMVEYFGEQLDGYVFSQGGWVQSYGSRCVKPPIL 539
Query: 523 IGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALR 582
GDISRP +TV+W YA SLTDKP+KGMLTGPVTIL WSF R+D R +Q+ALA+R
Sbjct: 540 FGDISRPRAMTVDWIAYAASLTDKPMKGMLTGPVTILNWSFVRDDQPRSESCRQLALAIR 599
Query: 583 DEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHM 642
+EV DLE AG+G+IQIDE ALREGLPLR+S W AYL W VE+FRI A D+TQIHTHM
Sbjct: 600 EEVLDLETAGVGVIQIDEAALREGLPLRKSQWQAYLDWAVESFRITANGVADETQIHTHM 659
Query: 643 CYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVE 702
CY EFNDI+ SIAA+DADVITIETSRSDMELL++F++F YPNEIGPGVYDIHSPN+P+
Sbjct: 660 CYSEFNDIIASIAAMDADVITIETSRSDMELLDAFDDFKYPNEIGPGVYDIHSPNIPTEG 719
Query: 703 WIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
I L+KKAA+RIPA+RLWVNPDCGLKTR W E AL NMV AA+ LR
Sbjct: 720 HIVDLMKKAAERIPADRLWVNPDCGLKTRQWAEVLPALTNMVSAAKTLR 768
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: 1703
Number of extensions: 74
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: 772
Length adjustment: 40
Effective length of query: 713
Effective length of database: 732
Effective search space: 521916
Effective search space used: 521916
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 AZOBR_RS24275 AZOBR_RS24275 (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.20254.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 1092.6 0.0 0 1092.4 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS24275 AZOBR_RS24275 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS24275 AZOBR_RS24275 5-methyltetrahydropteroyltriglutamate--homocysteine methyltra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1092.4 0.0 0 0 1 753 [. 7 769 .. 7 770 .. 0.98
Alignments for each domain:
== domain 1 score: 1092.4 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+kRelk+ale+ywkg +s++el +v +dlrk++++ q +d++pv+df++YD+vLd++
lcl|FitnessBrowser__azobra:AZOBR_RS24275 7 LGFPRIGAKRELKFALEAYWKGASSRDELVRVGADLRKRHWRDQG--ALDLVPVGDFAFYDQVLDMSFT 73
79****************************************998..58******************** PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek..............kdvaalemtkwfntnYhYlvPelsk 124
lg++per+k ++d+ ld+yF++aRG + +vaa emtkwf+tnYhY+vPe+++
lcl|FitnessBrowser__azobra:AZOBR_RS24275 74 LGNLPERVKGFHGDA--LDNYFRVARGRSAetaahsaeehggccGGVAAGEMTKWFDTNYHYIVPEFDA 140
**********97776..9*********98899************99*********************** PP
TIGR01371 125 eeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklae 193
++f+l++++lle++ eak++gv++kPv++Gp+t+l L+kak+ +++l+ll++llpvY +l+ l++
lcl|FitnessBrowser__azobra:AZOBR_RS24275 141 GTTFTLDASRLLEQLAEAKAQGVKAKPVIVGPVTYLALGKAKD--GSDKLALLPRLLPVYAGLLQALTD 207
******************************************8..5589******************** PP
TIGR01371 194 agvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDl 262
+gvewvqideP+lv++l++++++a+++ay++l ++klll+tYf++++++l + slpv++l+lD
lcl|FitnessBrowser__azobra:AZOBR_RS24275 208 QGVEWVQIDEPILVTELEAAWRDAFTQAYRALGT--GAVKLLLATYFGQLQDNLPLACSLPVQGLHLDA 274
********************************97..699****************************** PP
TIGR01371 263 veakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdle 331
++a++e ++ +++++d+v+++Gv++Grniwk+dl ++l+ l+ ++++ g++l++++scsllhvpvdl
lcl|FitnessBrowser__azobra:AZOBR_RS24275 275 ITARDEVDALIQALPTDRVVSLGVVNGRNIWKTDLGATLDWLEPVAERLGERLWIAPSCSLLHVPVDLA 343
********************************************************************* PP
TIGR01371 332 leekldkelkellafakekleelkvlkeale....g.eaavaealeaeaaaiaarkkskrvadekvker 395
e+kld+e +++lafa++klee++vl+ al+ g +aava++l+a++aa++ar++s+rv++ +vk++
lcl|FitnessBrowser__azobra:AZOBR_RS24275 344 GERKLDEEARSWLAFAVQKLEEIRVLAIALTpgrdGgRAAVAAELDANRAAVEARRHSPRVNNPAVKAA 412
***************************999644434578999*************************** PP
TIGR01371 396 lealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikee 464
++a++++ rr+s f eRa++q+ +lnlP +PtttiGsfPqtke+R+aR++f++g+i++ +Y+++++ e
lcl|FitnessBrowser__azobra:AZOBR_RS24275 413 VAAIDARLGRRKSAFIERAAKQATRLNLPKFPTTTIGSFPQTKEIRQARSQFKAGTIDAVAYTEAMRGE 481
********************************************************************* PP
TIGR01371 465 ikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmt 533
i++ ++ qe+lglDvLvhGe+eRnDmveyFge+l+G++f q gWvqsYGsRcvkPpi++gd+srp++mt
lcl|FitnessBrowser__azobra:AZOBR_RS24275 482 IARSVREQEALGLDVLVHGEAERNDMVEYFGEQLDGYVFSQGGWVQSYGSRCVKPPILFGDISRPRAMT 550
********************************************************************* PP
TIGR01371 534 vkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepa 602
v++++ya slt+kp+kGmLtGPvtilnWsfvR+D+pr+e+++q+ala+r+ev dLe ag+ +iqiDe+a
lcl|FitnessBrowser__azobra:AZOBR_RS24275 551 VDWIAYAASLTDKPMKGMLTGPVTILNWSFVRDDQPRSESCRQLALAIREEVLDLETAGVGVIQIDEAA 619
********************************************************************* PP
TIGR01371 603 lReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdm 671
lReglPlrks++++Yldwave+Fr++a+gv+detqihthmCYsefn+ii++iaa+daDvi+ie+srsdm
lcl|FitnessBrowser__azobra:AZOBR_RS24275 620 LREGLPLRKSQWQAYLDWAVESFRITANGVADETQIHTHMCYSEFNDIIASIAAMDADVITIETSRSDM 688
********************************************************************* PP
TIGR01371 672 elldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaa 740
ellda+++ +ky++eiG+GvyDihsp++P++ ++ +l++ka +++p++rlWvnPDCGLktR+w ev +a
lcl|FitnessBrowser__azobra:AZOBR_RS24275 689 ELLDAFDD-FKYPNEIGPGVYDIHSPNIPTEGHIVDLMKKAAERIPADRLWVNPDCGLKTRQWAEVLPA 756
********.77********************************************************** PP
TIGR01371 741 lknlveaakelRe 753
l+n+v aak+lR+
lcl|FitnessBrowser__azobra:AZOBR_RS24275 757 LTNMVSAAKTLRA 769
***********97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (772 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.07
# Mc/sec: 7.31
//
[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