Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_066918374.1 ACG33_RS02345 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_001579945.1:WP_066918374.1
Length = 764
Score = 834 bits (2154), Expect = 0.0
Identities = 431/760 (56%), Positives = 535/760 (70%), Gaps = 18/760 (2%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G +RELK A E+YW G +R E+ AV +LR RHWD Q + +D +PVGDFA
Sbjct: 5 HNLGFPRIGAQRELKFALEAYWQGQISRNEIEAVAAQLRKRHWDNQ--SALDWVPVGDFA 62
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEP--------AAAAEMTK 117
+YD +L S LGN+P R + G+ +D FR+ RGR+ AA EMTK
Sbjct: 63 FYDQMLDMSFTLGNLPERVRGFHGNT-LDNYFRVARGRSAEAAADHARCCGGVAAGEMTK 121
Query: 118 WFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQ 177
WF+TNYHY+VPEF +F+L ++LL ++ EA + G KPV++GP+T+L LGK K +
Sbjct: 122 WFDTNYHYIVPEFDAQSEFRLDASRLLVQLAEARSQGINAKPVIIGPITYLALGKAKDDS 181
Query: 178 FDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQV 236
D+L+LL +LPVYQ++L LA + + WVQIDEP LV EL W AY AY AL G+V
Sbjct: 182 -DKLALLPRLLPVYQELLTALAAQSVAWVQIDEPILVTELEDRWRQAYISAYAALNTGKV 240
Query: 237 KLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNV 296
KLLL TYF + NL + ALPVQG+H+D + + +V L RLP+D ++S G+I+GRN+
Sbjct: 241 KLLLATYFGPLLENLSLVGALPVQGIHLDAIRARQEVDPLVARLPADRIVSLGVIDGRNI 300
Query: 297 WRADLTEKYAQIKDIVGKRD--LWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCH 354
W+ D+ ++ + K LW+A SCSLLH P+DL+ E +LD E+KSW AFALQK
Sbjct: 301 WKTDINALLDWLEPLAMKLGDRLWIAPSCSLLHVPVDLTSEQKLDPEIKSWLAFALQKLD 360
Query: 355 ELALLRDALNSGDTAALAEWSA---PIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYE 411
EL + AL+ G A AE A I+ R S RV++P ++ +AAI A+ +R N Y
Sbjct: 361 ELHTVAAALDKGREAVTAELDANRTAIEMRHRSPRVNDPTIKAAVAAIDAEFGRRKNTYT 420
Query: 412 VRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVE 471
RA Q R KLP +PTTTIGSFPQT E+R R FK G +D Y + I++++ E
Sbjct: 421 QRALKQAVRLKLPKFPTTTIGSFPQTPEVRQARSRFKAGRIDQAAYHKAMRAEIERSVRE 480
Query: 472 QERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAP 531
QE LGLDV VHGEAERNDMVEYFGE LDG+ FT+ GWVQSYGSRCVKPPI+ GDISRP
Sbjct: 481 QESLGLDVFVHGEAERNDMVEYFGEQLDGYAFTRFGWVQSYGSRCVKPPILFGDISRPKA 540
Query: 532 ITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAA 591
+TVEW KYA SLTDKP+KGMLTGPVT+L WSF R+D R KQ+ALA+R EV DLE A
Sbjct: 541 MTVEWIKYAASLTDKPMKGMLTGPVTLLNWSFVRDDQPRSVSCKQLALAIRAEVLDLEKA 600
Query: 592 GIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIM 651
GI IIQIDE ALREGLPLR+S W +YL W VEAFRI A D+TQIHTHMCY EFNDI+
Sbjct: 601 GIRIIQIDEAALREGLPLRKSQWKSYLSWAVEAFRIAANGVADETQIHTHMCYSEFNDII 660
Query: 652 DSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKA 711
SIA +DADVITIETSRS MELL++F++F YPNEIGPGVYDIHSPN+P E I L++KA
Sbjct: 661 ASIADMDADVITIETSRSAMELLDAFDDFRYPNEIGPGVYDIHSPNIPRREHIVQLMRKA 720
Query: 712 AKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
A+R+PAERLWVNPDCGLKTR W E ALANMV AA+ LR
Sbjct: 721 AERVPAERLWVNPDCGLKTRQWSEVIPALANMVAAARELR 760
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: 1684
Number of extensions: 75
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: 764
Length adjustment: 40
Effective length of query: 713
Effective length of database: 724
Effective search space: 516212
Effective search space used: 516212
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 WP_066918374.1 ACG33_RS02345 (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.2527017.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 1095.6 0.0 0 1095.4 0.0 1.0 1 NCBI__GCF_001579945.1:WP_066918374.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001579945.1:WP_066918374.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1095.4 0.0 0 0 1 754 [] 7 762 .. 7 762 .. 0.99
Alignments for each domain:
== domain 1 score: 1095.4 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgai 73
lgfPrig++Relk+ale+yw+g+is++e+++va++lrk+++++q+ +d +pv+df++YD++Ld++ lg++
NCBI__GCF_001579945.1:WP_066918374.1 7 LGFPRIGAQRELKFALEAYWQGQISRNEIEAVAAQLRKRHWDNQS--ALDWVPVGDFAFYDQMLDMSFTLGNL 77
79*****************************************99..58************************ PP
TIGR01371 74 perfkeladdesdldtyFaiaRGtek..........kdvaalemtkwfntnYhYlvPelskeeefklsknkll 136
per++ ++++ ld+yF++aRG + +vaa emtkwf+tnYhY+vPe+++++ef+l++++ll
NCBI__GCF_001579945.1:WP_066918374.1 78 PERVRGFHGNT--LDNYFRVARGRSAeaaadharccGGVAAGEMTKWFDTNYHYIVPEFDAQSEFRLDASRLL 148
******96665..9*********98899*******999*********************************** PP
TIGR01371 137 eeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvld 209
++ ea+++g+++kPv++Gpit+l L+kak+ ++++l+ll++llpvY+e+l+ la+++v wvqideP+lv++
NCBI__GCF_001579945.1:WP_066918374.1 149 VQLAEARSQGINAKPVIIGPITYLALGKAKD--DSDKLALLPRLLPVYQELLTALAAQSVAWVQIDEPILVTE 219
******************************8..5689************************************ PP
TIGR01371 210 lskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvL 282
l++++++a+ +ay++l+ ++klll+tYf+ + e+l+ + lpv++++lD ++a++e + +a++++d+++
NCBI__GCF_001579945.1:WP_066918374.1 220 LEDRWRQAYISAYAALNT--GKVKLLLATYFGPLLENLSLVGALPVQGIHLDAIRARQEVDPLVARLPADRIV 290
****************97..699************************************************** PP
TIGR01371 283 vaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekleelk 355
++GvidGrniwk+d+++ l+ l+ l+ k gd+l++++scsllhvpvdl+ e+kld+e+k++lafa +kl+el+
NCBI__GCF_001579945.1:WP_066918374.1 291 SLGVIDGRNIWKTDINALLDWLEPLAMKLGDRLWIAPSCSLLHVPVDLTSEQKLDPEIKSWLAFALQKLDELH 363
************************************************************************* PP
TIGR01371 356 vlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllP 427
+++ al++ ++av+++l+a+++ai+ r++s+rv+d ++k++++a++++ rr++ +++Ra +q+ +l+lP +P
NCBI__GCF_001579945.1:WP_066918374.1 364 TVAAALDKgREAVTAELDANRTAIEMRHRSPRVNDPTIKAAVAAIDAEFGRRKNTYTQRALKQAVRLKLPKFP 436
******999**************************************************************** PP
TIGR01371 428 tttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaG 500
tttiGsfPqt evR+aR++f++g+i++++Y+k++++ei++ ++ qe+lglDv vhGe+eRnDmveyFge+l+G
NCBI__GCF_001579945.1:WP_066918374.1 437 TTTIGSFPQTPEVRQARSRFKAGRIDQAAYHKAMRAEIERSVREQESLGLDVFVHGEAERNDMVEYFGEQLDG 509
************************************************************************* PP
TIGR01371 501 faftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkei 573
+aft++gWvqsYGsRcvkPpi++gd+srpk+mtv+++kya slt+kp+kGmLtGPvt+lnWsfvR+D+pr+ +
NCBI__GCF_001579945.1:WP_066918374.1 510 YAFTRFGWVQSYGSRCVKPPILFGDISRPKAMTVEWIKYAASLTDKPMKGMLTGPVTLLNWSFVRDDQPRSVS 582
************************************************************************* PP
TIGR01371 574 aeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYse 646
++q+ala+r ev dLe+agi+iiqiDe+alReglPlrks++++Yl+waveaFr+aa+gv+detqihthmCYse
NCBI__GCF_001579945.1:WP_066918374.1 583 CKQLALAIRAEVLDLEKAGIRIIQIDEAALREGLPLRKSQWKSYLSWAVEAFRIAANGVADETQIHTHMCYSE 655
************************************************************************* PP
TIGR01371 647 fneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpke 719
fn+ii++ia++daDvi+ie+srs mellda+++ ++y++eiG+GvyDihsp++P e++ +l++ka +++p+e
NCBI__GCF_001579945.1:WP_066918374.1 656 FNDIIASIADMDADVITIETSRSAMELLDAFDD-FRYPNEIGPGVYDIHSPNIPRREHIVQLMRKAAERVPAE 727
*********************************.66************************************* PP
TIGR01371 720 rlWvnPDCGLktRkweevkaalknlveaakelRek 754
rlWvnPDCGLktR+w+ev++al n+v+aa+elR++
NCBI__GCF_001579945.1:WP_066918374.1 728 RLWVNPDCGLKTRQWSEVIPALANMVAAARELRAE 762
*********************************85 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (764 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 15.52
//
[ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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