Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate Synpcc7942_0411 Synpcc7942_0411 tryptophan synthase subunit alpha
Query= metacyc::MONOMER-3561 (251 letters) >FitnessBrowser__SynE:Synpcc7942_0411 Length = 266 Score = 185 bits (469), Expect = 9e-52 Identities = 96/240 (40%), Positives = 146/240 (60%), Gaps = 3/240 (1%) Query: 6 SLIPYLTAGDPSVEKTLEFLLAVE-EFAGLIELGIPFSDPMADGKTIQESHYRALRNGFK 64 +LIP+LTAGDP +E T + LLA++ E A LIELG+P+SDP+ADG IQ + RAL+ G + Sbjct: 18 ALIPFLTAGDPDLETTRQALLALDREGADLIELGVPYSDPLADGPVIQAAATRALQAGTR 77 Query: 65 LDDTFRILREFRRHSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSHAGE 124 LDD +L++ R P++L TY NP+ G + FL + A+GA+G++V DLP+ + Sbjct: 78 LDDVLALLKDVRSQIKAPIVLFTYCNPILNRGFEAFLDQIAAAGANGLVVPDLPLEESQR 137 Query: 125 FLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLPETAFEFVR 184 + A E G+ + L AP + +R+ I K + GF+YL+S+ G TG R + + ++ Sbjct: 138 LSEVAAERGIDLILLIAPTSSADRIAAISKQARGFIYLVSVTGVTGMRQGMQSRVADLLQ 197 Query: 185 RARKICNNKLAVGFGVSRREQVEELLKAGADGVVVGSALIELISRSENPVEELRRKVAEL 244 R+ + + VGFG+S EQ ++ GADGV+VGSA + + E VE + EL Sbjct: 198 EIRQGTDKPIGVGFGISGAEQARQVRDWGADGVIVGSAFVNRL--QEQGVEGVATLCREL 255 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: 182 Number of extensions: 5 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: 251 Length of database: 266 Length adjustment: 24 Effective length of query: 227 Effective length of database: 242 Effective search space: 54934 Effective search space used: 54934 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 Synpcc7942_0411 Synpcc7942_0411 (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.7670.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-95 304.2 0.0 2.9e-95 304.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0411 Synpcc7942_0411 tryptophan synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0411 Synpcc7942_0411 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 304.0 0.0 2.9e-95 2.9e-95 1 237 [. 8 243 .. 8 260 .. 0.97 Alignments for each domain: == domain 1 score: 304.0 bits; conditional E-value: 2.9e-95 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++l++++ +a++pF+tagdPdle++ +++ l ++Gad++ElGvp+sDPlaDGp+iqaa++RAl+ag+ lcl|FitnessBrowser__SynE:Synpcc7942_0411 8 FAALRSQGRCALIPFLTAGDPDLETTRQALLALDREGADLIELGVPYSDPLADGPVIQAAATRALQAGT 76 78999**************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++++l+llk vr++ +++Pivl+ty n+i+++g e+F++++++ag +g++v+DlPlee+++l e+a++ lcl|FitnessBrowser__SynE:Synpcc7942_0411 77 RLDDVLALLKDVRSQ-IKAPIVLFTYCNPILNRGFEAFLDQIAAAGANGLVVPDLPLEESQRLSEVAAE 144 **************9.***************************************************** PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 +g++ i+l+aPt++ +r+ +i+++++Gf+Ylvsv+Gvtg r+ ++++v +l++++++ ++kP+ vGFGi lcl|FitnessBrowser__SynE:Synpcc7942_0411 145 RGIDLILLIAPTSSADRIAAISKQARGFIYLVSVTGVTGMRQGMQSRVADLLQEIRQGTDKPIGVGFGI 213 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieek 237 s +eq+++++++gadgvivGsA+v++++e+ lcl|FitnessBrowser__SynE:Synpcc7942_0411 214 SGAEQARQVRDWGADGVIVGSAFVNRLQEQ 243 *************************99887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (266 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: 9.22 // [ok]
This GapMind analysis is from Apr 09 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