Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_011318709.1 AVA_RS09645 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000204075.1:WP_011318709.1 Length = 413 Score = 126 bits (317), Expect = 1e-33 Identities = 115/356 (32%), Positives = 163/356 (45%), Gaps = 35/356 (9%) Query: 72 IGRPTPLFRAKRLEEYLKTP----ARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHV 127 +GR TPL+ A+RL + P A+IY K E TG+HKIN A+ Q AK G + + Sbjct: 67 VGRATPLYFAERLTAHYARPDGTGAQIYLKREDLNHTGAHKINNALGQVLLAKRMGKQRI 126 Query: 128 VTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEY 187 + ETGAGQ G A A + + ++ I+M E++ + M+L GA V E Sbjct: 127 IAETGAGQHGVATATVCARFGLECVIYMGVHDMERQALNVFRMRLMGAEV-----RPVEA 181 Query: 188 GRKILETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQE 239 G G+L A SEAI + N Y++GSV +V +VIGQE Sbjct: 182 G----------TGTLKDATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFHAVIGQE 231 Query: 240 TITQ-LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKY 298 T Q L+ G DIL+ CVGGGSN G Y F+ N+ R I V +A ++ Sbjct: 232 TRAQALEKWGGLPDILLACVGGGSNAMGLFYEFV-NESSIRLIGVEAAGEGVNTEKHAAT 290 Query: 299 DFPDSAGLLPLVKMITLGKD---YVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNER 355 G+L L + + + GL Y GV P S L G E+ + Sbjct: 291 LTKGRVGVLHGAMSYLLQDEDGQVIEAHSISAGLDYPGVGPEHSYLKDVGRAEYYSVTDE 350 Query: 356 EIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDL 411 + A + +GI+PA E+AHAI A ++ + R I+ N SG G D+ Sbjct: 351 QALAAFQRLSRLEGIIPALETAHAI-AYLETLCPQLDGSPR--IIINCSGRGDKDV 403 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: 384 Number of extensions: 24 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: 413 Length adjustment: 32 Effective length of query: 393 Effective length of database: 381 Effective search space: 149733 Effective search space used: 149733 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_011318709.1 AVA_RS09645 (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.7789.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-194 629.9 0.1 9.2e-194 629.7 0.1 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011318709.1 AVA_RS09645 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011318709.1 AVA_RS09645 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.7 0.1 9.2e-194 9.2e-194 1 383 [. 21 408 .. 21 410 .. 0.98 Alignments for each domain: == domain 1 score: 629.7 bits; conditional E-value: 9.2e-194 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklg..... 64 g+fg+fGG+yvpe+l++al+ele+ay+k+++d+ f++el++ll++y+gr+tpl+fa++l+ ++ lcl|NCBI__GCF_000204075.1:WP_011318709.1 21 GRFGRFGGKYVPETLMPALAELETAYQKYRHDPGFQAELQQLLRDYVGRATPLYFAERLTAHYArpdgt 89 78**********************************************************987522223 PP TIGR00263 65 gakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaed 133 ga+iylkredl+htGahkinnalgq+llakr+Gk+riiaetGaGqhGvatat++a++glec++ymG +d lcl|NCBI__GCF_000204075.1:WP_011318709.1 90 GAQIYLKREDLNHTGAHKINNALGQVLLAKRMGKQRIIAETGAGQHGVATATVCARFGLECVIYMGVHD 158 689****************************************************************** PP TIGR00263 134 verqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsv 202 +erq+lnvfrm+l+ga+v pv+ G+ tlkda++ea+rdWvt+ve+thy+lGs++GphP+P +vr+f +v lcl|NCBI__GCF_000204075.1:WP_011318709.1 159 MERQALNVFRMRLMGAEVRPVEAGTGTLKDATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFHAV 227 ********************************************************************* PP TIGR00263 203 igeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGke 271 ig+e+++q lek g lPd+++acvGGGsna+G+f++f+++++++ligvea+G+G++tekhaatl+kG++ lcl|NCBI__GCF_000204075.1:WP_011318709.1 228 IGQETRAQALEKWGGLPDILLACVGGGSNAMGLFYEFVNESSIRLIGVEAAGEGVNTEKHAATLTKGRV 296 ********************************************************************* PP TIGR00263 272 GvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGi 340 GvlhGa+++llqdedGq+ eahs+saGldypgvgPeh++l++ graey ++tde+al+a+++ls+ eGi lcl|NCBI__GCF_000204075.1:WP_011318709.1 297 GVLHGAMSYLLQDEDGQVIEAHSISAGLDYPGVGPEHSYLKDVGRAEYYSVTDEQALAAFQRLSRLEGI 365 ********************************************************************* PP TIGR00263 341 ipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 ipale++ha+a+le l+p+l+ +++n sGrGdkd++tvak lcl|NCBI__GCF_000204075.1:WP_011318709.1 366 IPALETAHAIAYLETLCPQLDGSPRIIINCSGRGDKDVQTVAK 408 *****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (413 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.56 // [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