Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate WP_012968450.1 KVAR_RS15180 tryptophan synthase subunit alpha
Query= metacyc::MONOMER-3561 (251 letters) >NCBI__GCF_000025465.1:WP_012968450.1 Length = 269 Score = 155 bits (393), Expect = 6e-43 Identities = 88/251 (35%), Positives = 136/251 (54%), Gaps = 5/251 (1%) Query: 3 EKGSLIPYLTAGDPSVEKTLEFLLA-VEEFAGLIELGIPFSDPMADGKTIQESHYRALRN 61 ++G+ +P++T GDP E++L+ + A +E A +ELGIPFSDP+ADG TIQ + RA Sbjct: 15 QEGAFVPFVTLGDPGPEQSLKIIDALIEGGADALELGIPFSDPLADGPTIQGAALRAFAA 74 Query: 62 GFKLDDTFRILREFR-RHSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVS 120 G F +L R +H + P+ L+ Y N VF G+ F + G D +LV D+PV Sbjct: 75 GVTPAQCFEMLAAIRQKHPTIPIGLLMYANLVFSPGIDAFYAQCARVGVDSVLVADVPVE 134 Query: 121 HAGEFLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLPETAF 180 + F AA + +F+ PN D+ LR+I G+ YL+S G TGA +R Sbjct: 135 ESASFRQAAMRHNIAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLH 194 Query: 181 EFVRRARKICNNKLAVGFGVSRREQVEELLKAGADGVVVGSALIELISRSENPVEELRRK 240 V + + GFG+S EQV + AGA G + GSA++++I R ++E + Sbjct: 195 HLVEKLAEYHAAPPLQGFGISAPEQVSAAIDAGAAGAISGSAIVKIIERH---LDEPQTM 251 Query: 241 VAELSGYSRAL 251 + EL + ++L Sbjct: 252 LDELKAFVQSL 262 Lambda K H 0.319 0.138 0.386 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: 174 Number of extensions: 8 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: 251 Length of database: 269 Length adjustment: 24 Effective length of query: 227 Effective length of database: 245 Effective search space: 55615 Effective search space used: 55615 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_012968450.1 KVAR_RS15180 (tryptophan synthase subunit alpha)
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.9492.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-112 359.8 0.0 3.1e-112 359.6 0.0 1.0 1 lcl|NCBI__GCF_000025465.1:WP_012968450.1 KVAR_RS15180 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_012968450.1 KVAR_RS15180 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.6 0.0 3.1e-112 3.1e-112 1 256 [] 8 263 .. 8 263 .. 1.00 Alignments for each domain: == domain 1 score: 359.6 bits; conditional E-value: 3.1e-112 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++lk+++e afvpFvt+gdP e+sl+ii+ l++ GadalElG+pfsDPlaDGptiq a+lRA++agv lcl|NCBI__GCF_000025465.1:WP_012968450.1 8 FAQLKNHQEGAFVPFVTLGDPGPEQSLKIIDALIEGGADALELGIPFSDPLADGPTIQGAALRAFAAGV 76 789****************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 ++++++e+l+++r+k+++iPi+ll+y+nl+f+ g+++Fya+++ +gvd+vlvaD+P+ee++++++aa + lcl|NCBI__GCF_000025465.1:WP_012968450.1 77 TPAQCFEMLAAIRQKHPTIPIGLLMYANLVFSPGIDAFYAQCARVGVDSVLVADVPVEESASFRQAAMR 145 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 h++++if+++P+a+++ l++ia++++G++Yl+s+aGvtga++r++ +++l++k+ ++ ++P l+GFGi lcl|NCBI__GCF_000025465.1:WP_012968450.1 146 HNIAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLHHLVEKLAEYHAAPPLQGFGI 214 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkelk 256 s++eqv +++++ga+g+i+GsA+vkiie++ld+++ +l+el++fv++lk lcl|NCBI__GCF_000025465.1:WP_012968450.1 215 SAPEQVSAAIDAGAAGAISGSAIVKIIERHLDEPQTMLDELKAFVQSLK 263 **********************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (269 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: 8.08 // [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