Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate WP_010959711.1 MCA_RS01725 aminomethyltransferase
Query= CharProtDB::CH_000563 (364 letters) >NCBI__GCF_000008325.1:WP_010959711.1 Length = 360 Score = 386 bits (991), Expect = e-112 Identities = 196/364 (53%), Positives = 249/364 (68%), Gaps = 9/364 (2%) Query: 1 MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60 M + T L+E+H GARM +F GW +PLHYGSQI EHHAVR AGMFDVSH+ +VD+ G Sbjct: 1 MGRCTALHEEHLALGARMTEFSGWELPLHYGSQIAEHHAVRRAAGMFDVSHLGVVDVEGL 60 Query: 61 RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120 + FLR +LANDVA+L + G+ LY MLN GG++DDL+V + + FRL++N+ TREK Sbjct: 61 QAAPFLRRVLANDVARLAEPGRMLYGCMLNQDGGIVDDLVVGFIDDRRFRLILNAGTREK 120 Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180 DLSW+ + A PF + +T RDDL+MIA+QGP++ A + G+KPF Q G Sbjct: 121 DLSWLHRQAAPFSVTVTPRDDLAMIALQGPDSPRIADAVV----AAGSSGLKPFTATQRG 176 Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240 D FIA TGYTGE G+EI LP+ +A WR L +AG +PCGLGARDTLRLEAGM LYGQ+M Sbjct: 177 DRFIARTGYTGEDGFEIILPHAEAGSLWRQLFQAGARPCGLGARDTLRLEAGMRLYGQDM 236 Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGT-EKLVGLVMTEKGVLRNELPVR 299 DET++PLA +GWT+AWEP +RDFIGR ALE +R G+ K VGL++ E G+LR+ V Sbjct: 237 DETVTPLACGLGWTVAWEPEERDFIGRAALERERIGGSPSKFVGLILEEPGILRSGQKV- 295 Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359 A N EG++TSG FSPTL SI LARVP G V+IR V KP FVR Sbjct: 296 ---AVANVGEGVVTSGGFSPTLRRSIGLARVPAATGRECRVEIRGSLKRATVVKPRFVRR 352 Query: 360 GKAV 363 ++ Sbjct: 353 STSL 356 Lambda K H 0.320 0.136 0.402 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: 396 Number of extensions: 14 Number of successful extensions: 4 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: 364 Length of database: 360 Length adjustment: 29 Effective length of query: 335 Effective length of database: 331 Effective search space: 110885 Effective search space used: 110885 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: 49 (23.5 bits)
Align candidate WP_010959711.1 MCA_RS01725 (aminomethyltransferase)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))
# 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.carbon/TIGR00528.hmm # target sequence database: /tmp/gapView.2555.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00528 [M=362] Accession: TIGR00528 Description: gcvT: glycine cleavage system T protein 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-126 407.2 0.0 3.3e-126 407.0 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010959711.1 MCA_RS01725 aminomethyltransfera Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010959711.1 MCA_RS01725 aminomethyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 407.0 0.0 3.3e-126 3.3e-126 4 362 .] 5 352 .. 2 352 .. 0.98 Alignments for each domain: == domain 1 score: 407.0 bits; conditional E-value: 3.3e-126 TIGR00528 4 tpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanD 72 t+L++ h lg+++++f+GwelP++y+s+i eh+avr +aG+fDvsh+g v+++G ++ fL+r+lanD lcl|NCBI__GCF_000008325.1:WP_010959711.1 5 TALHEEHLALGARMTEFSGWELPLHYGSQIAEHHAVRRAAGMFDVSHLGVVDVEGLQAAPFLRRVLAND 73 9******************************************************************** PP TIGR00528 73 vdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlske 140 v++L++ G+ +y +ln +GG+vDDl+v + +d+rf+l++na+t+ekDl+wl+ ++++++ t +++ lcl|NCBI__GCF_000008325.1:WP_010959711.1 74 VARLAEpGRMLYGCMLNQDGGIVDDLVVG-FIDDRRFRLILNAGTREKDLSWLHRQAAPFSVTVTPRDD 141 ****988******************9986.55666********************************** PP TIGR00528 141 isllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwk 209 ++++alqGP++ i + ++ + +glk+f+ q+++ +iartGytGedGfei+++ +a lw+ lcl|NCBI__GCF_000008325.1:WP_010959711.1 142 LAMIALQGPDSPRIADAVVAAGSSGLKPFTATQRGDR-----FIARTGYTGEDGFEIILPHAEAGSLWR 205 ********************************99998.....*************************** PP TIGR00528 210 klveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkeng 278 +l +a g +P+GLgarDtLrleagm LyGq++de++tPl+ glgw+v++e++++dfiGra+le + g lcl|NCBI__GCF_000008325.1:WP_010959711.1 206 QLFQA-GARPCGLGARDTLRLEAGMRLYGQDMDETVTPLACGLGWTVAWEPEERDFIGRAALERERIGG 273 *****.*************************************************************** PP TIGR00528 279 tekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrn 347 + +k vGl + e gi+r + kv ++ +G+vtsG +sPtL +i+la+v+ + G++ ve+r+ lcl|NCBI__GCF_000008325.1:WP_010959711.1 274 SPSKFVGLILEEPGILRSGQKVAV--ANVGEGVVTSGGFSPTLRRSIGLARVP---AATGRECRVEIRG 337 ************************..5569***********************...899********** PP TIGR00528 348 klvkikvvkklfvrs 362 l ++ vvk+ fvr+ lcl|NCBI__GCF_000008325.1:WP_010959711.1 338 SLKRATVVKPRFVRR 352 ************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (362 nodes) Target sequences: 1 (360 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.37 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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