Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate CA265_RS05025 CA265_RS05025 tryptophan synthase subunit alpha
Query= uniprot:A0A3N7DTH5 (255 letters) >FitnessBrowser__Pedo557:CA265_RS05025 Length = 255 Score = 404 bits (1037), Expect = e-117 Identities = 196/254 (77%), Positives = 222/254 (87%) Query: 1 MNRINKLFQEKKNILSIYYTAGYPNLGDTVAIAEELERSGADLLEIGFPYSDPVADGPVI 60 MNRI +LFQEKKNILSIYYTAGYPN GDT+ IAE LE+SGAD+LEIGFPYSDPVADGPVI Sbjct: 1 MNRIKQLFQEKKNILSIYYTAGYPNTGDTLQIAEALEQSGADMLEIGFPYSDPVADGPVI 60 Query: 61 QASSKTALDGGMTLKLLFEQLKDLRKTVNIPVLLMGYVNPMLQYGVENFCKSCAEVGVDG 120 QASSK +LD GMTL+LLFEQLKDLRK V IPVLLMGYVNP+LQ+GVE FC++CAEVGVDG Sbjct: 61 QASSKQSLDQGMTLQLLFEQLKDLRKKVTIPVLLMGYVNPVLQFGVEKFCEACAEVGVDG 120 Query: 121 CIVPDLPMVEYEELYSGVFEANGLTNIFLVTPQTSTERIRKIDGLSNGFIYLLSSSATTG 180 CIVPDLPMVEYEE Y FE + L+N+FL+TPQT+ ERI KIDGL+NGFIYLLSSSATTG Sbjct: 121 CIVPDLPMVEYEEFYKDCFEKHNLSNVFLITPQTAEERIHKIDGLTNGFIYLLSSSATTG 180 Query: 181 QNLQVSENTEAYFSRIAEMKLNNPTMIGFGISSKETFDKACQYANGAIIGSAFVKSLKSG 240 +NL+V TEAYFSRI + L NPTMIGFGIS K+TFDKAC YANGAIIG+AFVK++ G Sbjct: 181 KNLEVGNTTEAYFSRIKNLNLKNPTMIGFGISDKQTFDKACSYANGAIIGTAFVKAIADG 240 Query: 241 KVTDSVKDFMKTFK 254 + +SV +FMK FK Sbjct: 241 NLAESVSNFMKKFK 254 Lambda K H 0.317 0.135 0.382 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: 320 Number of extensions: 8 Number of successful extensions: 1 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
Align candidate CA265_RS05025 CA265_RS05025 (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.31434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-73 230.3 0.0 1e-72 230.1 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS05025 CA265_RS05025 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS05025 CA265_RS05025 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 230.1 0.0 1e-72 1e-72 3 239 .. 6 241 .. 4 255 .] 0.94 Alignments for each domain: == domain 1 score: 230.1 bits; conditional E-value: 1e-72 TIGR00262 3 tlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvk 70 +l +++++ + ++tag+P++ +l+i++ l ++Gad+lE+G+p+sDP+aDGp+iqa+++ l++g++ lcl|FitnessBrowser__Pedo557:CA265_RS05025 6 QLFQEKKNILSIYYTAGYPNTGDTLQIAEALEQSGADMLEIGFPYSDPVADGPVIQASSKQSLDQGMT 73 667788889999******************************************************** PP TIGR00262 71 vekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaa.k 137 ++ +e lk +r+k ++iP+ l+ y n++++ gve+F + ++e+gvdg +v+DlP+ e +++++ + + lcl|FitnessBrowser__Pedo557:CA265_RS05025 74 LQLLFEQLKDLRKK-VTIPVLLMGYVNPVLQFGVEKFCEACAEVGVDGCIVPDLPMVEYEEFYKDCfE 140 **************.*************************************************9978 PP TIGR00262 138 khgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkals.kkPvlvG 204 kh+++++fl++P++ eer++ki+ ++Gf+Yl+s++ tg + +v +++++ ++k+l+ k P ++G lcl|FitnessBrowser__Pedo557:CA265_RS05025 141 KHNLSNVFLITPQTAEERIHKIDGLTNGFIYLLSSSATTGKNLEVGNTTEAYFSRIKNLNlKNPTMIG 208 9*********************************************************98578***** PP TIGR00262 205 FGiskkeqvkelkelgadgvivGsAlvkiieekld 239 FGis k+ ++ + a+g+i+G A+vk i++ + lcl|FitnessBrowser__Pedo557:CA265_RS05025 209 FGISDKQTFDKACSY-ANGAIIGTAFVKAIADG-N 241 **************9.899***********986.3 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.90 // [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