Align candidate WP_012779310.1 TERTU_RS12440 (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.21360.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-171 555.3 0.0 4.5e-171 555.1 0.0 1.0 1 lcl|NCBI__GCF_000023025.1:WP_012779310.1 TERTU_RS12440 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_012779310.1 TERTU_RS12440 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 555.1 0.0 4.5e-171 4.5e-171 1 384 [. 7 392 .. 7 393 .. 0.99 Alignments for each domain: == domain 1 score: 555.1 bits; conditional E-value: 4.5e-171 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g fgefGG+yvpe+l +al +le+ y+++++de+f++e+ +l +e++grptplt ++ls+ lggaki+ lcl|NCBI__GCF_000023025.1:WP_012779310.1 7 GLFGEFGGRYVPEILRPALCQLEDMYQQLRSDETFWQEYLQLTQEFSGRPTPLTALPRLSELLGGAKIW 75 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+h+Gahkinn+lgqall+kr+Gk+riiaetGaGqhG+ata++aa++gl+ ++ymG+edverq lcl|NCBI__GCF_000023025.1:WP_012779310.1 76 LKREDLNHSGAHKINNVLGQALLVKRMGKQRIIAETGAGQHGLATAIIAARMGLQATIYMGSEDVERQY 144 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 nvf+m++lga+vvpv++Gs+tlkda++ealrdW++sv+dthyvlG+a+Gp+PfPe+v fq+vi++e+ lcl|NCBI__GCF_000023025.1:WP_012779310.1 145 SNVFWMRQLGAEVVPVNHGSCTLKDALDEALRDWAASVDDTHYVLGTACGPAPFPELVTYFQRVISQEI 213 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlsk..GkeGvl 274 ++q +++ g lP+av+acvGGGsna+G+f +f+++++v+l+gveagG+ + +h+ +l+ ++G+ lcl|NCBI__GCF_000023025.1:WP_012779310.1 214 RAQAKHQIGALPNAVVACVGGGSNALGAFCDFLDEPSVRLLGVEAGGRSQQPGQHSIRLHGdlASPGIA 282 ***********************************************************8622579*** PP TIGR00263 275 hGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipa 343 +G+kt +lq+ +Gq+ e+hs++aGldy+gv+P +a l+ +gr+ +++td+e+ +a++ll++ eGiipa lcl|NCBI__GCF_000023025.1:WP_012779310.1 283 QGYKTLFLQNRNGQLGETHSIAAGLDYVGVSPVLADLVARGRVDATSATDAEVTHAFQLLMRYEGIIPA 351 ********************************************************************* PP TIGR00263 344 lesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 lesshala la++++ +e vv+nlsGrGdkd++++a+a lcl|NCBI__GCF_000023025.1:WP_012779310.1 352 LESSHALAGGFALAKEMQPQEHVVINLSGRGDKDIFNIAQA 392 *************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (430 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: 11.62 // [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