Align candidate WP_038208391.1 Q392_RS13825 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))
# 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/TIGR00263.hmm # target sequence database: /tmp/gapView.31459.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00263 [M=385] Accession: TIGR00263 Description: trpB: tryptophan synthase, beta subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-191 620.9 0.1 5.1e-191 620.7 0.1 1.0 1 lcl|NCBI__GCF_000745855.1:WP_038208391.1 Q392_RS13825 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038208391.1 Q392_RS13825 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 620.7 0.1 5.1e-191 5.1e-191 1 383 [. 12 404 .. 12 406 .. 0.97 Alignments for each domain: == domain 1 score: 620.7 bits; conditional E-value: 5.1e-191 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG +v+e+l +a++el++ay+++k+d++f++e+ + lk+++grp+p+++a++ s+++gga+iy lcl|NCBI__GCF_000745855.1:WP_038208391.1 12 GHFGPYGGSFVSETLTHAIAELRDAYDRYKDDPAFQAEFAYELKHFVGRPSPVYHAARTSREIGGAQIY 80 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn++gqa+la+r+Gk r+iaetGaGqhGvatat++a+ glec+vymG+edv+rq+ lcl|NCBI__GCF_000745855.1:WP_038208391.1 81 LKREDLNHTGAHKINNVIGQAMLARRMGKPRVIAETGAGQHGVATATICARYGLECVVYMGSEDVKRQS 149 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv+rm+llga+vvpv+sGs+tlkda+nea+rdWvt+ve+t+y++G+++GphP+P++vr+fqsvig+e+ lcl|NCBI__GCF_000745855.1:WP_038208391.1 150 PNVYRMNLLGATVVPVESGSRTLKDALNEAMRDWVTNVENTFYIIGTVAGPHPYPAMVRDFQSVIGNEC 218 ********************************************************************* PP TIGR00263 208 keqi....l......ekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatl 266 eq+ + e+egr Pd+v+acvGGGsna+G+f+++i + v+l+gvea+G+G+d+ kh+a++ lcl|NCBI__GCF_000745855.1:WP_038208391.1 219 IEQMpamlAaqgitgEAEGRQPDVVVACVGGGSNAMGVFHPYIPFPGVRLVGVEAAGQGLDSGKHSASI 287 9997333212222235689************************************************** PP TIGR00263 267 skGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealklls 335 ++G++GvlhG++t++lq+edGqi+e+hs+saGldypgvgPeha+la+t+raey+ +tdeeal+a+++l+ lcl|NCBI__GCF_000745855.1:WP_038208391.1 288 QRGSPGVLHGNRTYILQNEDGQITETHSISAGLDYPGVGPEHAWLADTKRAEYVGVTDEEALAAFHHLC 356 ********************************************************************* PP TIGR00263 336 keeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 ++eGiipalessha+a++ kla++++ d+ ++vnlsGrGdkd+ tva+ lcl|NCBI__GCF_000745855.1:WP_038208391.1 357 RTEGIIPALESSHAMAYALKLAKTMRPDQSILVNLSGRGDKDIGTVAD 404 *********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (426 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.20 // [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