Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013817320.1 METME_RS03010 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000214665.1:WP_013817320.1 Length = 400 Score = 141 bits (355), Expect = 4e-38 Identities = 123/408 (30%), Positives = 182/408 (44%), Gaps = 59/408 (14%) Query: 29 PQGAYFSRIDLLRSILPKEVLRQQFTI--ERYIKIPEEVRDRYLSIGRPTPLFRAKRLEE 86 P G F L+ +I Q++ + E ++ ++RD +GRP+PL+ A+R E Sbjct: 16 PYGGIFVAETLMPAITELNEAYQRYLVDPEFIAELDADLRDY---VGRPSPLYHAQRWSE 72 Query: 87 YLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASM 146 +L A+IY K E TG+HK+N + QA AK G ++ ETGAGQ G A A A+ Sbjct: 73 HLGG-AQIYLKREDLNHTGAHKVNNTVGQALLAKRMGKTRIIAETGAGQHGVATATVAAR 131 Query: 147 YNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKILETNPQHPGSLGIAM 206 ++ ++M V ++ + M+L GA V A E G K L+ A+ Sbjct: 132 LGLECVVYMGAVDVARQALNVYRMKLLGATVVA-----VESGSKTLKD----------AL 176 Query: 207 SEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ-LDLLGEDADILIGC 257 +EA+ + N Y++G+V +V Q+VIG+E Q +D G D L+ C Sbjct: 177 NEALRDWVTNIDNTFYIIGTVAGPHPYPAMVRDFQAVIGREAKQQCIDQAGRLPDALVAC 236 Query: 258 VGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEIPKFSKGEYKYDFPDS 303 VGGGSN G YPFI +K K R+ A A P G Y D Sbjct: 237 VGGGSNAIGLFYPFIDDKSVKMYGVEAAGDGIDTGRHSAPLCAGRPGVLHGNRTYLMADD 296 Query: 304 AGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKI 363 G + + + GL Y GV P S L G + + E Sbjct: 297 DG------------EIIETHSISAGLDYPGVGPEHSWLKDTGRANYVNITDDEALAGFHA 344 Query: 364 FIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDL 411 +GI+PA ES+HA+ + A RK+ ++I+ NLSG G D+ Sbjct: 345 LTRMEGIIPALESSHALAYTMKLAPTMRKD---QIIIVNLSGRGDKDM 389 Lambda K H 0.318 0.138 0.403 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: 360 Number of extensions: 15 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: 425 Length of database: 400 Length adjustment: 31 Effective length of query: 394 Effective length of database: 369 Effective search space: 145386 Effective search space used: 145386 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_013817320.1 METME_RS03010 (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.27189.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-199 647.0 0.1 6.1e-199 646.8 0.1 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013817320.1 METME_RS03010 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013817320.1 METME_RS03010 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 646.8 0.1 6.1e-199 6.1e-199 1 384 [. 12 395 .. 12 396 .. 1.00 Alignments for each domain: == domain 1 score: 646.8 bits; conditional E-value: 6.1e-199 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG +v+e+l++a++el++ay+++ d+ef +el+ l++y+grp+pl++a++ s++lgga+iy lcl|NCBI__GCF_000214665.1:WP_013817320.1 12 GHFGPYGGIFVAETLMPAITELNEAYQRYLVDPEFIAELDADLRDYVGRPSPLYHAQRWSEHLGGAQIY 80 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahk+nn++gqallakr+Gk+riiaetGaGqhGvatat+aa+lglec+vymGa dv+rq+ lcl|NCBI__GCF_000214665.1:WP_013817320.1 81 LKREDLNHTGAHKVNNTVGQALLAKRMGKTRIIAETGAGQHGVATATVAARLGLECVVYMGAVDVARQA 149 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 lnv+rm+llga+vv+v+sGsktlkda+nealrdWvt++++t+y++G+++GphP+P++vr+fq+vig+e+ lcl|NCBI__GCF_000214665.1:WP_013817320.1 150 LNVYRMKLLGATVVAVESGSKTLKDALNEALRDWVTNIDNTFYIIGTVAGPHPYPAMVRDFQAVIGREA 218 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 k+q +++grlPda++acvGGGsnaiG+f++fi+d++v+++gvea+G Gidt +h+a l +G++GvlhG lcl|NCBI__GCF_000214665.1:WP_013817320.1 219 KQQCIDQAGRLPDALVACVGGGSNAIGLFYPFIDDKSVKMYGVEAAGDGIDTGRHSAPLCAGRPGVLHG 287 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+l+ d+dG+i e+hs+saGldypgvgPeh++l++tgra+y++itd+eal+++++l++ eGiipale lcl|NCBI__GCF_000214665.1:WP_013817320.1 288 NRTYLMADDDGEIIETHSISAGLDYPGVGPEHSWLKDTGRANYVNITDDEALAGFHALTRMEGIIPALE 356 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 sshala+ +klap+++kd+i++vnlsGrGdkd++t++++ lcl|NCBI__GCF_000214665.1:WP_013817320.1 357 SSHALAYTMKLAPTMRKDQIIIVNLSGRGDKDMHTIMQR 395 ************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (400 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: 12.10 // [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