Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_101443593.1 BD749_RS02800 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_002846395.1:WP_101443593.1 Length = 396 Score = 141 bits (356), Expect = 3e-38 Identities = 116/367 (31%), Positives = 177/367 (48%), Gaps = 39/367 (10%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRPTPL+ AKRL E T IY K E TG+HKIN I Q AK G ++ ET Sbjct: 55 VGRPTPLYFAKRLSEKYNT--NIYLKREDLNHTGAHKINNTIGQILLAKRLGKTRIIAET 112 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A ++ N++ ++M +V E++ + M++ GA V + + G K Sbjct: 113 GAGQHGVATATVCALMNLECIVYMGEVDVERQAPNVARMKMLGATVVPATS-----GSKT 167 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVL------DVVLLHQSVIGQETITQ 243 L+ A +EAI + N + Y++GSV+ D+V Q+VI +E +Q Sbjct: 168 LKD----------ATNEAIRDWINNPEDTYYIIGSVVGPHPYPDMVARFQAVISEEMKSQ 217 Query: 244 L--DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFP 301 L E+ D ++ CVGGGSN G Y ++ + K +A +A + S Sbjct: 218 LLEKTGSENPDYIVACVGGGSNAAGAFYHYLDTPEVK-LVAAEAAGLGIDSGESAATSVL 276 Query: 302 DSAGLL---PLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIF 358 G++ + M T P + GL Y GV P + L + G + + E Sbjct: 277 GKEGIIHGSRTLLMQTEDGQVTEPYSISAGLDYPGVGPLHAHLHQSGRAIFESITDEEAL 336 Query: 359 EAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418 +A +GI+PA E+AHA+ A+ + A+ + +V+V NLSG G DL+ Y + Sbjct: 337 QAVLELTRLEGIIPALETAHALAAI--GRLGAKPD---EVVVINLSGRGDKDLATY---L 388 Query: 419 KRLNGNG 425 R N +G Sbjct: 389 DRFNFDG 395 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: 377 Number of extensions: 22 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: 425 Length of database: 396 Length adjustment: 31 Effective length of query: 394 Effective length of database: 365 Effective search space: 143810 Effective search space used: 143810 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_101443593.1 BD749_RS02800 (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.3554437.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-184 597.2 0.0 8.1e-184 597.0 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101443593.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101443593.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 597.0 0.0 8.1e-184 8.1e-184 1 381 [. 9 387 .. 9 391 .. 0.99 Alignments for each domain: == domain 1 score: 597.0 bits; conditional E-value: 8.1e-184 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 g++g+fGG+yvpe+l +++eel+++y ++ ++++f++el+ llk+y+grptpl+fak+ls+k++ ++iylkre NCBI__GCF_002846395.1:WP_101443593.1 9 GFYGRFGGAYVPEMLYPNVEELRQNYLTIMAEPDFQEELQALLKDYVGRPTPLYFAKRLSEKYN-TNIYLKRE 80 68*************************************************************8.******** PP TIGR00263 74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146 dl+htGahkinn++gq+llakrlGk+riiaetGaGqhGvatat++al++lec vymG+ dverq++nv rm++ NCBI__GCF_002846395.1:WP_101443593.1 81 DLNHTGAHKINNTIGQILLAKRLGKTRIIAETGAGQHGVATATVCALMNLECIVYMGEVDVERQAPNVARMKM 153 ************************************************************************* PP TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqileke.grl 218 lga+vvp tsGsktlkda+nea+rdW+ + edt+y++Gs+vGphP+P++v +fq+vi+ee+k+q+lek + NCBI__GCF_002846395.1:WP_101443593.1 154 LGATVVPATSGSKTLKDATNEAIRDWINNPEDTYYIIGSVVGPHPYPDMVARFQAVISEEMKSQLLEKTgSEN 226 *******************************************************************997899 PP TIGR00263 219 PdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqiee 291 Pd+++acvGGGsna G+f+++++++ev+l++ ea+G+Gid+ + aat GkeG++hG++t l+q+edGq++e NCBI__GCF_002846395.1:WP_101443593.1 227 PDYIVACVGGGSNAAGAFYHYLDTPEVKLVAAEAAGLGIDSGESAATSVLGKEGIIHGSRTLLMQTEDGQVTE 299 ************************************************************************* PP TIGR00263 292 ahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkde 364 +s+saGldypgvgP ha+l+++gra +e+itdeeal+a+ l++ eGiipale++halaa+ +l + k de NCBI__GCF_002846395.1:WP_101443593.1 300 PYSISAGLDYPGVGPLHAHLHQSGRAIFESITDEEALQAVLELTRLEGIIPALETAHALAAIGRLGA--KPDE 370 ****************************************************************998..789* PP TIGR00263 365 ivvvnlsGrGdkdletv 381 +vv+nlsGrGdkdl+t NCBI__GCF_002846395.1:WP_101443593.1 371 VVVINLSGRGDKDLATY 387 **************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (396 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: 00:00:00.00 # Mc/sec: 26.40 // [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