Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_022949611.1 H035_RS0114095 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_000421465.1:WP_022949611.1 Length = 273 Score = 257 bits (656), Expect = 2e-73 Identities = 139/267 (52%), Positives = 177/267 (66%), Gaps = 3/267 (1%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 MSRI F LK R LIPF+TAGDP PE V ++HA+ AGAD++ELGVPFSDPMAD Sbjct: 1 MSRIQTTFENLKREKRKALIPFITAGDPRPEFTVPMLHAMAAAGADILELGVPFSDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GPVIQ ASERA+ V L VL VA FR+ D TPIVLMGYLNP+E GY FA A + Sbjct: 61 GPVIQRASERALTHHVSLHQVLDMVAEFRRRDIQTPIVLMGYLNPLERMGYRAFAEAARK 120 Query: 121 AGVDGVLLVDCPLE--ESAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSF 178 AGVDGVL VD P E E+ +L L +AG+ I L APT+ R+ + + G+LYYVS Sbjct: 121 AGVDGVLTVDLPPEEAEAEMLPLLYEAGIDPIFLLAPTSTRGRIEKADAAGRGYLYYVSL 180 Query: 179 AGITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDR 238 G+TGA HL ++A +V ++RA A+ P+ VGFG+++A +A +A ADAVV+GSALV + Sbjct: 181 KGVTGAGHLDLEEVARKVEEIRAAARLPIGVGFGVKNAETAAKMAQLADAVVVGSALVQK 240 Query: 239 L-AGATDAGEITRRTQAFLAPIRAALD 264 + + D I A L +RAA+D Sbjct: 241 VEENSGDPERIETAIVALLKEMRAAMD 267 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: 221 Number of extensions: 7 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: 266 Length of database: 273 Length adjustment: 25 Effective length of query: 241 Effective length of database: 248 Effective search space: 59768 Effective search space used: 59768 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_022949611.1 H035_RS0114095 (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.20972.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-79 250.6 0.0 6.5e-79 250.4 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022949611.1 H035_RS0114095 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022949611.1 H035_RS0114095 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.4 0.0 6.5e-79 6.5e-79 1 256 [] 8 263 .. 8 263 .. 0.98 Alignments for each domain: == domain 1 score: 250.4 bits; conditional E-value: 6.5e-79 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 fe+lk+++ ka++pF+tagdP e ++ +++ ++ aGad+lElGvpfsDP+aDGp+iq+a+ RAl++ v lcl|NCBI__GCF_000421465.1:WP_022949611.1 8 FENLKREKRKALIPFITAGDPRPEFTVPMLHAMAAAGADILELGVPFSDPMADGPVIQRASERALTHHV 76 899****************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleead.dlleaak 137 +++++l++++++r++ ++ Pivl+ y n++ ++g +F + a++agvdgvl +DlP eea+ ++l lcl|NCBI__GCF_000421465.1:WP_022949611.1 77 SLHQVLDMVAEFRRRDIQTPIVLMGYLNPLERMGYRAFAEAARKAGVDGVLTVDLPPEEAEaEMLPLLY 145 **********************************************************98736889999 PP TIGR00262 138 khgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFG 206 + g+++ifl aPt+ r++k + ++G+ Y vs Gvtga + eev + +++++a ++ P+ vGFG lcl|NCBI__GCF_000421465.1:WP_022949611.1 146 EAGIDPIFLLAPTSTRGRIEKADAAGRGYLYYVSLKGVTGAGHLDLEEVARKVEEIRAAARLPIGVGFG 214 *******************************************99999********************* PP TIGR00262 207 iskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkelk 256 + ++e + ++ +l ad+v+vGsAlv+++ee+ +d+e++ ++ ++ ke++ lcl|NCBI__GCF_000421465.1:WP_022949611.1 215 VKNAETAAKMAQL-ADAVVVGSALVQKVEENSGDPERIETAIVALLKEMR 263 *************.899***********************9999999885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (273 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.96 // [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