Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate Echvi_2511 Echvi_2511 tryptophan synthase, alpha subunit
Query= uniprot:A0A3N7DTH5 (255 letters) >FitnessBrowser__Cola:Echvi_2511 Length = 258 Score = 302 bits (774), Expect = 4e-87 Identities = 145/242 (59%), Positives = 189/242 (78%), Gaps = 1/242 (0%) Query: 1 MNRINKLFQEKK-NILSIYYTAGYPNLGDTVAIAEELERSGADLLEIGFPYSDPVADGPV 59 MNRI++LFQEKK NILSIY+TAG+P L DT+AI E +E +GAD++E+G PYSDPVADGP Sbjct: 1 MNRIDQLFQEKKGNILSIYFTAGFPKLDDTLAIMEAIEGAGADIIEVGMPYSDPVADGPT 60 Query: 60 IQASSKTALDGGMTLKLLFEQLKDLRKTVNIPVLLMGYVNPMLQYGVENFCKSCAEVGVD 119 IQ S+K AL+ GM +K +F+QL+ +R+TV IPV+LMGY+NP+LQYG+E FCK C EVGVD Sbjct: 61 IQESNKAALENGMNMKKMFQQLEKMRETVTIPVVLMGYLNPILQYGIEAFCKKCNEVGVD 120 Query: 120 GCIVPDLPMVEYEELYSGVFEANGLTNIFLVTPQTSTERIRKIDGLSNGFIYLLSSSATT 179 G IVPDLP+ +Y++ Y +F+ L N FL++PQTS ERIR+ID S+GFIY++SS + T Sbjct: 121 GLIVPDLPIQQYQDDYKALFDEYDLRNTFLISPQTSEERIREIDQQSDGFIYMVSSHSIT 180 Query: 180 GQNLQVSENTEAYFSRIAEMKLNNPTMIGFGISSKETFDKACQYANGAIIGSAFVKSLKS 239 G +S+ EAYF R+ M+L NP +IGFGIS TF KA Y++GAIIGSAF+K L + Sbjct: 181 GAKSGISDEQEAYFERVKSMELENPRLIGFGISDHATFSKASSYSHGAIIGSAFIKVLSN 240 Query: 240 GK 241 K Sbjct: 241 AK 242 Lambda K H 0.317 0.135 0.382 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: 230 Number of extensions: 6 Number of successful extensions: 2 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: 255 Length of database: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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: 47 (22.7 bits)
Align candidate Echvi_2511 Echvi_2511 (tryptophan synthase, alpha subunit)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha 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/TIGR00262.hmm # target sequence database: /tmp/gapView.17632.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00262 [M=256] Accession: TIGR00262 Description: trpA: tryptophan synthase, alpha 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-76 241.7 0.1 3.4e-76 241.5 0.1 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2511 Echvi_2511 tryptophan synthase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2511 Echvi_2511 tryptophan synthase, alpha subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 241.5 0.1 3.4e-76 3.4e-76 4 242 .. 8 246 .. 5 257 .. 0.93 Alignments for each domain: == domain 1 score: 241.5 bits; conditional E-value: 3.4e-76 TIGR00262 4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 +++k+ + + ++tag P+l+ +l i++ + aGad++E+G+p+sDP+aDGptiq++++ Al++g++++k+++ lcl|FitnessBrowser__Cola:Echvi_2511 8 FQEKKGNILSIYFTAGFPKLDDTLAIMEAIEGAGADIIEVGMPYSDPVADGPTIQESNKAALENGMNMKKMFQQ 81 567788888899************************************************************** PP TIGR00262 78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPlee.addlleaakkhgvkqiflvaPt 150 l+k+re+ ++iP+vl+ y n+i+++g+e+F +k++e+gvdg++v+DlP+++ +dd+ ++++++ fl++P+ lcl|FitnessBrowser__Cola:Echvi_2511 82 LEKMRET-VTIPVVLMGYLNPILQYGIEAFCKKCNEVGVDGLIVPDLPIQQyQDDYKALFDEYDLRNTFLISPQ 154 ******9.*****************************************982456677789************* PP TIGR00262 151 aeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkals.kkPvlvGFGiskkeqvkelkelgadg 223 ++eer+++i+++s+Gf+Y+vs+ +tga++ +++e ++ ++vk++ + P l+GFGis + ++ + + g lcl|FitnessBrowser__Cola:Echvi_2511 155 TSEERIREIDQQSDGFIYMVSSHSITGAKSGISDEQEAYFERVKSMElENPRLIGFGISDHATFSKASSY-SHG 227 ********************************************986489******************99.889 PP TIGR00262 224 vivGsAlvkiieeklddee 242 +i+GsA++k++++ +d + lcl|FitnessBrowser__Cola:Echvi_2511 228 AIIGSAFIKVLSNAKDLKA 246 ***********99987433 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (258 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: 00:00:00.00 # Mc/sec: 8.28 // [ok]
This GapMind analysis is from Apr 09 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