Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate WP_066328927.1 BLR17_RS13320 tryptophan synthase subunit beta
Query= BRENDA::Q97TX6 (429 letters) >NCBI__GCF_900100165.1:WP_066328927.1 Length = 393 Score = 135 bits (341), Expect = 2e-36 Identities = 124/405 (30%), Positives = 182/405 (44%), Gaps = 61/405 (15%) Query: 43 LKEVLPSKVLELEFAKERYVKIP---------DEVLERYLQVGRPTPIIRAKRLEEYLGN 93 + E+L V EL +++Y+KI D++L+ Y VGRP+P+ AKRL E Sbjct: 19 IPEMLYPNVEEL---RQQYLKIMAEPDFKAEFDQLLKDY--VGRPSPLYFAKRLSEKY-- 71 Query: 94 NIKIYLKMESYTYTGSHKINSALAHVYYAKLDNAKFVTTETGAGQWGSSVALASALFRMK 153 N KIYLK E +TG+HKIN+ + + AK K + ETGAGQ G + A AL ++ Sbjct: 72 NTKIYLKREDLNHTGAHKINNTIGQILVAKKLGKKRIIAETGAGQHGVATATVCALMGLE 131 Query: 154 AHIFMVRTSYYAKPYRKYMMQMYGAEVHPSPSDLTEFGRQLLAKDSNHPGSLGIAISDAV 213 ++M + M+M GA V P+ S G + L +N AI D + Sbjct: 132 CIVYMGEIDIARQAPNVARMKMLGATVRPALS-----GSRTLKDATNE------AIRDWI 180 Query: 214 EYAHKNGGKYVVGSVVNSD------IMFKTIAGMEAKKQM-ELIG-EDPDYIIGVVGGGS 265 + Y++GS + F+++ E K Q+ E G E+PDY++ +GGGS Sbjct: 181 N--NPVDTHYIIGSAIGPHPYPDMVTRFQSVISEEIKWQLKEKEGRENPDYVVACIGGGS 238 Query: 266 NYAALAYPFLGDELRSGKVRRKYIASGSSEVPKMTKGVYKYDYPDTAKL--------LPM 317 N A Y FL + G V KG++ T+KL Sbjct: 239 NAAGTFYHFLHEP-----------EVGIIAVEAAGKGIHSGHSAATSKLGKVGIIHGCKT 287 Query: 318 LKMYTIGSDFVPPPVYAGGLRYHGVAPTLSLLISKGIVQARDYSQEESFKWAKLFSELEG 377 L M T P + GL Y GV P + L G + + +++ + +LEG Sbjct: 288 LLMQTPDGQITEPYSISAGLDYPGVGPMHAHLAETGRAEFFSVTDDDAMQAGLELCKLEG 347 Query: 378 YIPAPETSHALPILAEIAEEAKKSGERKTVLVSFSGHGLLDLGNY 422 IPA E+SHAL +L + KK V++ SG G DL NY Sbjct: 348 IIPAIESSHALAVLND-----KKFKPEDVVVICLSGRGDKDLNNY 387 Lambda K H 0.316 0.135 0.392 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: 415 Number of extensions: 28 Number of successful extensions: 5 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: 429 Length of database: 393 Length adjustment: 31 Effective length of query: 398 Effective length of database: 362 Effective search space: 144076 Effective search space used: 144076 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_066328927.1 BLR17_RS13320 (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.818201.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-181 588.2 0.0 4.5e-181 588.0 0.0 1.0 1 NCBI__GCF_900100165.1:WP_066328927.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066328927.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 588.0 0.0 4.5e-181 4.5e-181 1 383 [. 9 389 .. 9 391 .. 0.98 Alignments for each domain: == domain 1 score: 588.0 bits; conditional E-value: 4.5e-181 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g++g+fGG+y+pe+l +++eel+++y k+ ++++fk+e+++llk+y+grp+pl+fak+ls+k++ +kiylkre NCBI__GCF_900100165.1:WP_066328927.1 9 GYYGQFGGAYIPEMLYPNVEELRQQYLKIMAEPDFKAEFDQLLKDYVGRPSPLYFAKRLSEKYN-TKIYLKRE 80 79*************************************************************8.******** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 dl+htGahkinn++gq+l+ak+lGkkriiaetGaGqhGvatat++al+glec vymG+ d++rq++nv rm++ NCBI__GCF_900100165.1:WP_066328927.1 81 DLNHTGAHKINNTIGQILVAKKLGKKRIIAETGAGQHGVATATVCALMGLECIVYMGEIDIARQAPNVARMKM 153 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqileke.grl 218 lga+v p sGs+tlkda+nea+rdW+ + dthy++Gsa+GphP+P++v +fqsvi+ee+k+q++eke + NCBI__GCF_900100165.1:WP_066328927.1 154 LGATVRPALSGSRTLKDATNEAIRDWINNPVDTHYIIGSAIGPHPYPDMVTRFQSVISEEIKWQLKEKEgREN 226 *********************************************************************5568 PP TIGR00263 219 PdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqiee 291 Pd+v+ac+GGGsna G+f++f++++ev +i+vea+GkGi++ + aat + Gk+G++hG kt l+q+ dGqi+e NCBI__GCF_900100165.1:WP_066328927.1 227 PDYVVACIGGGSNAAGTFYHFLHEPEVGIIAVEAAGKGIHSGHSAATSKLGKVGIIHGCKTLLMQTPDGQITE 299 ************************************************************************* PP TIGR00263 292 ahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkde 364 +s+saGldypgvgP ha+laetgrae+ ++td++a++a l+k eGiipa+esshala+l+ k k ++ NCBI__GCF_900100165.1:WP_066328927.1 300 PYSISAGLDYPGVGPMHAHLAETGRAEFFSVTDDDAMQAGLELCKLEGIIPAIESSHALAVLNDK--KFKPED 370 *************************************************************9865..458899 PP TIGR00263 365 ivvvnlsGrGdkdletvak 383 +vv+ lsGrGdkdl++ ++ NCBI__GCF_900100165.1:WP_066328927.1 371 VVVICLSGRGDKDLNNYIE 389 **************98665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 26.33 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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