Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_057687221.1 ABB28_RS15195 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_001431535.1:WP_057687221.1 Length = 269 Score = 300 bits (769), Expect = 2e-86 Identities = 164/267 (61%), Positives = 194/267 (72%), Gaps = 2/267 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 +SR+D RF L+ A R LIPF+TAGDPS E V +MHALV+AGAD++ELGVPFSDPMAD Sbjct: 3 VSRLDARFQRLRDAQRKALIPFITAGDPSLEATVPVMHALVEAGADVLELGVPFSDPMAD 62 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ +SERA+A+G GL VL VA FR D+DTP+VLMGYLNP+E HGYARFA EAV Sbjct: 63 GPTIQRSSERALARGAGLRYVLQAVAEFRSRDSDTPVVLMGYLNPVEIHGYARFATEAVA 122 Query: 121 AGVDGVLLVDCPLEESAVLQPLRD-AGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AGVDG+LLVD P EE+ D AGL +LLA+PTT +R L G A G+LYYVSFA Sbjct: 123 AGVDGILLVDLPPEEAHEANEAFDAAGLALVLLASPTTSDARADTLLGLARGYLYYVSFA 182 Query: 180 GITGAAHLSTGDIA-ARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDR 238 G+TGA+ L D A AR+ +RARA PV GFGI+DA SA A+A AD VV+GSALV Sbjct: 183 GVTGASDLLDHDAAGARLQALRARASVPVVAGFGIKDAGSAAAMARQADGVVVGSALVSV 242 Query: 239 LAGATDAGEITRRTQAFLAPIRAALDA 265 LA AT + + AFLAP+R ALDA Sbjct: 243 LAQATTVEDAVQAAGAFLAPLRQALDA 269 Lambda K H 0.322 0.136 0.394 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: 280 Number of extensions: 12 Number of successful extensions: 3 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: 266 Length of database: 269 Length adjustment: 25 Effective length of query: 241 Effective length of database: 244 Effective search space: 58804 Effective search space used: 58804 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_057687221.1 ABB28_RS15195 (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.17382.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-73 232.1 0.0 2.8e-73 231.9 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057687221.1 ABB28_RS15195 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057687221.1 ABB28_RS15195 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.9 0.0 2.8e-73 2.8e-73 1 252 [. 10 260 .. 10 264 .. 0.95 Alignments for each domain: == domain 1 score: 231.9 bits; conditional E-value: 2.8e-73 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f+ l++++ ka++pF+tagdP+le ++ +++ lv+aGad+lElGvpfsDP+aDGptiq+++ RAl++g lcl|NCBI__GCF_001431535.1:WP_057687221.1 10 FQRLRDAQRKALIPFITAGDPSLEATVPVMHALVEAGADVLELGVPFSDPMADGPTIQRSSERALARGA 78 78899**************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 ++ +l+ ++++r++ s+ P+vl+ y n++ +g F ++a +agvdg+l++DlP eea+++ ea lcl|NCBI__GCF_001431535.1:WP_057687221.1 79 GLRYVLQAVAEFRSRDSDTPVVLMGYLNPVEIHGYARFATEAVAAGVDGILLVDLPPEEAHEANEAFDA 147 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveee.vkelikkvkalskkPvlvGFG 206 g++ ++l++Pt+++ r ++ ++G+ Y vs aGvtga++ ++++ + + ++ ++a +++Pv+ GFG lcl|NCBI__GCF_001431535.1:WP_057687221.1 148 AGLALVLLASPTTSDARADTLLGLARGYLYYVSFAGVTGASDLLDHDaAGARLQALRARASVPVVAGFG 216 ********************************************88746789***************** PP TIGR00262 207 iskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefv 252 i + + ++ adgv+vGsAlv ++++ + e a+++ +f lcl|NCBI__GCF_001431535.1:WP_057687221.1 217 IKDAGSAAAMARQ-ADGVVVGSALVSVLAQA-TTVEDAVQAAGAFL 260 ****999988887.9*************999.56777777766665 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.34 // [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