Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate WP_028950920.1 Q385_RS0106670 tryptophan synthase subunit alpha
Query= metacyc::MONOMER-3561 (251 letters) >NCBI__GCF_000619805.1:WP_028950920.1 Length = 255 Score = 172 bits (435), Expect = 8e-48 Identities = 97/241 (40%), Positives = 146/241 (60%), 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 LICYFMAGYPSVEDSIKTAFTLIENGADILEVGFPFSDPVADGTTIQIAHEKAVKDGITP 71 Query: 66 DDTFRILREFR-RHSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSHAGE 124 + F+I + + ++ + P+I M+YYNP+FR G + F AK SG DG +V DLP Sbjct: 72 EKVFQITKTIKEKYPNIPLIGMSYYNPIFRLGEENFCNRAKESGIDGFIVPDLPPEEGES 131 Query: 125 FLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLPETAF-EFV 183 A +GL +FL AP + +ER++ + K S F+Y +SL G TG RD LP E + Sbjct: 132 LKKVANSKGLSLIFLLAPTSNEERIKLVSKMSDDFIYYVSLTGITGERDTLPWNELREKI 191 Query: 184 RRARKICNNKLAVGFGVSRREQVEELLKAGADGVVVGSALIELISRSENPVEELRRKVAE 243 R I + K+AVGFGVS+ E +++ ADGV+VGS++++L + + E L+ V E Sbjct: 192 ATIRIITDKKIAVGFGVSKGEHA-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: 189 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_028950920.1 Q385_RS0106670 (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.14780.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-82 259.9 0.1 1e-81 259.6 0.1 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950920.1 Q385_RS0106670 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950920.1 Q385_RS0106670 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.6 0.1 1e-81 1e-81 9 237 .. 9 237 .. 3 254 .. 0.94 Alignments for each domain: == domain 1 score: 259.6 bits; conditional E-value: 1e-81 TIGR00262 9 ekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 k ++ ++ ag+P++e s++ + tl+++Gad+lE+G+pfsDP+aDG+tiq a+ +A+k+g+++ek++++ lcl|NCBI__GCF_000619805.1:WP_028950920.1 9 RKPLICYFMAGYPSVEDSIKTAFTLIENGADILEVGFPFSDPVADGTTIQIAHEKAVKDGITPEKVFQI 77 5779***************************************************************** PP TIGR00262 78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqifl 146 +k ++ek++niP++ ++yyn+if+ g+e+F ++ake+g+dg +v+DlP ee ++l ++a+++g++ ifl lcl|NCBI__GCF_000619805.1:WP_028950920.1 78 TKTIKEKYPNIPLIGMSYYNPIFRLGEENFCNRAKESGIDGFIVPDLPPEEGESLKKVANSKGLSLIFL 146 ********************************************************************* PP TIGR00262 147 vaPtaeeerlkkiaekseGfvYlvsvaGvtgarerve.eevkelikkvkalskkPvlvGFGiskkeqvk 214 aPt++eer+k +++ s+ f+Y vs +G+tg+r+ + +e++e i++++ +++k ++vGFG+sk e++k lcl|NCBI__GCF_000619805.1:WP_028950920.1 147 LAPTSNEERIKLVSKMSDDFIYYVSLTGITGERDTLPwNELREKIATIRIITDKKIAVGFGVSKGEHAK 215 ***********************************973669**************************** PP TIGR00262 215 elkelgadgvivGsAlvkiieek 237 + ++ adgvivGs +vk+ ++ lcl|NCBI__GCF_000619805.1:WP_028950920.1 216 IISQI-ADGVIVGSSVVKLQGKR 237 99999.9**********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: 9.43 // [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