Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate N515DRAFT_0116 N515DRAFT_0116 tryptophan synthase, alpha chain
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__Dyella79:N515DRAFT_0116 Length = 266 Score = 431 bits (1107), Expect = e-125 Identities = 219/266 (82%), Positives = 238/266 (89%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 M+RIDRRF LK+ RTGLIPFVTAGDP+PEH VALMHALVDAGAD+IELGVPFSDPMAD Sbjct: 1 MNRIDRRFDTLKSNRRTGLIPFVTAGDPAPEHTVALMHALVDAGADVIELGVPFSDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GPVIQHASERAIAKGVGLADVLGWV+ FRQ DADTP+VLMGYLNP+E GY RFA EAV+ Sbjct: 61 GPVIQHASERAIAKGVGLADVLGWVSTFRQRDADTPVVLMGYLNPVEIRGYERFAAEAVE 120 Query: 121 AGVDGVLLVDCPLEESAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAG 180 AGVDGVLLVDCPLEESAVL PL+ AGL++ILLAAPTT P+RMAQLCG+AEGFLYYVSFAG Sbjct: 121 AGVDGVLLVDCPLEESAVLAPLKAAGLRQILLAAPTTAPARMAQLCGAAEGFLYYVSFAG 180 Query: 181 ITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLA 240 ITGA LST DIAARVA +R+RAKAPVAVGFG+RDA SA+ IAGFADAVVIGSALV+RLA Sbjct: 181 ITGAGRLSTSDIAARVAGIRSRAKAPVAVGFGVRDAQSARDIAGFADAVVIGSALVERLA 240 Query: 241 GATDAGEITRRTQAFLAPIRAALDAR 266 GA A EI R +AFL PIR ALDAR Sbjct: 241 GAERADEIADRAKAFLQPIRTALDAR 266 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: 322 Number of extensions: 12 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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 N515DRAFT_0116 N515DRAFT_0116 (tryptophan synthase, alpha chain)
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.25994.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-72 229.2 0.0 2.3e-72 228.9 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0116 N515DRAFT_0116 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0116 N515DRAFT_0116 tryptophan synthase, alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 228.9 0.0 2.3e-72 2.3e-72 1 253 [. 8 257 .. 8 260 .. 0.95 Alignments for each domain: == domain 1 score: 228.9 bits; conditional E-value: 2.3e-72 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlk 66 f+tlk+++ + ++pFvtagdP e+++ +++ lv+aGad++ElGvpfsDP+aDGp+iq+a+ RA++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0116 8 FDTLKSNRRTGLIPFVTAGDPAPEHTVALMHALVDAGADVIELGVPFSDPMADGPVIQHASERAIA 73 789999************************************************************ PP TIGR00262 67 agvkvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddl 132 +gv ++++l + +r++ + P+vl+ y n++ +g e F a+a eagvdgvl++D Plee++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0116 74 KGVGLADVLGWVSTFRQRDADTPVVLMGYLNPVEIRGYERFAAEAVEAGVDGVLLVDCPLEESAV- 138 *************************************************************9975. PP TIGR00262 133 leaakkhgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalsk 198 l k g++qi+l+aPt+ + r+ ++ +eGf Y vs aG+tga + ++++ + ++ +++ +k lcl|FitnessBrowser__Dyella79:N515DRAFT_0116 139 LAPLKAAGLRQILLAAPTTAPARMAQLCGAAEGFLYYVSFAGITGAGRLSTSDIAARVAGIRSRAK 204 5678999*********************************************************** PP TIGR00262 199 kPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvk 253 +Pv+vGFG+ ++ ++++ + ad+v++GsAlv++++ + +++ ++ ++f + lcl|FitnessBrowser__Dyella79:N515DRAFT_0116 205 APVAVGFGVRDAQSARDIAGF-ADAVVIGSALVERLAGA-ERADEIADRAKAFLQ 257 ********************9.899**********9987.556666666666665 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.81 // [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