Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate WP_012674352.1 SULAZ_RS01860 tryptophan synthase subunit alpha
Query= metacyc::MONOMER-3561 (251 letters) >NCBI__GCF_000021545.1:WP_012674352.1 Length = 255 Score = 179 bits (455), Expect = 4e-50 Identities = 100/241 (41%), Positives = 149/241 (61%), Gaps = 6/241 (2%) Query: 7 LIPYLTAGDPSVEKTLEFLLA-VEEFAGLIELGIPFSDPMADGKTIQESHYRALRNGFKL 65 LI Y AG PSVE +++ +E A ++E+G PFSDP+ADG TIQ +H +A+++G Sbjct: 12 LICYFMAGYPSVEDSIKTAFTLIENGADILEVGFPFSDPVADGVTIQVAHEKAVKDGITP 71 Query: 66 DDTFRILREFR-RHSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSHAGE 124 + F+I + + ++ + P+I MTYYNP+FR G + F AK SG DG +V DLP G Sbjct: 72 EKVFQITKTIKEKYPNVPLIGMTYYNPIFRFGEENFCNRAKESGIDGFIVPDLPPEEGGN 131 Query: 125 FLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLP-ETAFEFV 183 A +GL +FL AP + +ER++ + K S F+Y +SL G TG RD LP + E + Sbjct: 132 LKKVANRKGLSLIFLLAPTSNEERIKLVSKMSDDFIYYVSLTGITGERDTLPWDELKEKI 191 Query: 184 RRARKICNNKLAVGFGVSRREQVEELLKAGADGVVVGSALIELISRSENPVEELRRKVAE 243 RKI + K+AVGFGVS+ E +++ ADGV+VGS++++L + + E L+ V E Sbjct: 192 TLIRKITDKKIAVGFGVSKGEHA-KIISQIADGVIVGSSVVKL--QGKRDFEGLKNLVKE 248 Query: 244 L 244 L Sbjct: 249 L 249 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: 186 Number of extensions: 13 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: 255 Length adjustment: 24 Effective length of query: 227 Effective length of database: 231 Effective search space: 52437 Effective search space used: 52437 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: 46 (22.3 bits)
Align candidate WP_012674352.1 SULAZ_RS01860 (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.1269988.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-81 259.4 0.1 1.5e-81 259.0 0.1 1.0 1 NCBI__GCF_000021545.1:WP_012674352.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021545.1:WP_012674352.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.0 0.1 1.5e-81 1.5e-81 9 237 .. 9 237 .. 4 254 .. 0.94 Alignments for each domain: == domain 1 score: 259.0 bits; conditional E-value: 1.5e-81 TIGR00262 9 ekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkkv 81 k ++ ++ ag+P++e s++ + tl+++Gad+lE+G+pfsDP+aDG tiq a+ +A+k+g+++ek+++++k + NCBI__GCF_000021545.1:WP_012674352.1 9 RKPLICYFMAGYPSVEDSIKTAFTLIENGADILEVGFPFSDPVADGVTIQVAHEKAVKDGITPEKVFQITKTI 81 5779********************************************************************* PP TIGR00262 82 rekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154 +ek++n+P++ +tyyn+if+ g+e+F ++ake+g+dg +v+DlP ee ++l ++a+++g++ ifl aPt++ee NCBI__GCF_000021545.1:WP_012674352.1 82 KEKYPNVPLIGMTYYNPIFRFGEENFCNRAKESGIDGFIVPDLPPEEGGNLKKVANRKGLSLIFLLAPTSNEE 154 ************************************************************************* PP TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerve.eevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgviv 226 r+k +++ s+ f+Y vs +G+tg+r+ + +e+ke i ++++++k ++vGFG+sk e++k + ++ adgviv NCBI__GCF_000021545.1:WP_012674352.1 155 RIKLVSKMSDDFIYYVSLTGITGERDTLPwDELKEKITLIRKITDKKIAVGFGVSKGEHAKIISQI-ADGVIV 226 ***************************973569****************************99999.9***** PP TIGR00262 227 GsAlvkiieek 237 Gs +vk+ ++ NCBI__GCF_000021545.1:WP_012674352.1 227 GSSVVKLQGKR 237 *****975544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (255 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: 20.94 // [ok]
This GapMind analysis is from Jul 25 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