Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate NP_349754.1 CA_C3157 tryptophan synthase subunit alpha
Query= uniprot:A0A3N7DTH5 (255 letters) >NCBI__GCF_000008765.1:NP_349754.1 Length = 263 Score = 180 bits (456), Expect = 3e-50 Identities = 101/238 (42%), Positives = 147/238 (61%), Gaps = 7/238 (2%) Query: 2 NRINKLFQE----KKNILSIYYTAGYPNLGDTVAIAEELERSGADLLEIGFPYSDPVADG 57 N+I+ F+E K + + T+GYP++ T I E+E+SGADL+E+G PYSDPVADG Sbjct: 3 NKIDLKFKELKYKNKKAMIPFVTSGYPDVETTKKIVIEMEKSGADLIELGIPYSDPVADG 62 Query: 58 PVIQASSKTALDGGMTLKLLFEQLKDLRKTVNIPVLLMGYVNPMLQYGVENFCKSCAEVG 117 P+IQ SS AL+ G+ +K + +K++RK V IP++ MGY + +YG+E F K E G Sbjct: 63 PIIQISSSGALNNGLKIKDIMNMVKEVRKNVKIPIVYMGYFGCVFKYGLEKFIKDSKESG 122 Query: 118 VDGCIVPDLPMVEYEELYSGVFEANGLTNIFLVTPQTSTERIRKIDGLSNGFIYLLSSSA 177 VDG ++PDLP+ E E + + + I LV P TS +RI KI + GFIY +S++ Sbjct: 123 VDGIVIPDLPLEERERV-KEIADRYEFYIIPLVAP-TSEDRIGKIVNGAKGFIYCVSTNG 180 Query: 178 TTGQNLQVSENTEAYFSRIAEMKLNNPTMIGFGISSKETFDKACQYANGAIIGSAFVK 235 TG ++ + +AY +++ N P IGFGISS E K +Y +G IIGSA +K Sbjct: 181 VTGVRNIIANDVKAYIDVVSKAS-NVPKCIGFGISSPEMAQKMKEYCDGVIIGSAVMK 237 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: 217 Number of extensions: 11 Number of successful extensions: 3 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: 263 Length adjustment: 24 Effective length of query: 231 Effective length of database: 239 Effective search space: 55209 Effective search space used: 55209 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 NP_349754.1 CA_C3157 (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.3387.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-86 274.7 1.5 2.8e-86 274.5 1.5 1.0 1 lcl|NCBI__GCF_000008765.1:NP_349754.1 CA_C3157 tryptophan synthase sub Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008765.1:NP_349754.1 CA_C3157 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 274.5 1.5 2.8e-86 2.8e-86 1 254 [. 9 258 .. 9 260 .. 0.98 Alignments for each domain: == domain 1 score: 274.5 bits; conditional E-value: 2.8e-86 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkve 72 f++lk k++ka++pFvt g+Pd+e++ +i+ + k+Gad++ElG+p+sDP+aDGp iq ++ Al++g+k++ lcl|NCBI__GCF_000008765.1:NP_349754.1 9 FKELKYKNKKAMIPFVTSGYPDVETTKKIVIEMEKSGADLIELGIPYSDPVADGPIIQISSSGALNNGLKIK 80 799********************************************************************* PP TIGR00262 73 kalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqi 144 ++++++k+vr++ ++iPiv + y+ +fk+g+e+F++ ke+gvdg++++DlPlee +++ e a +++ i lcl|NCBI__GCF_000008765.1:NP_349754.1 81 DIMNMVKEVRKN-VKIPIVYMGYFGCVFKYGLEKFIKDSKESGVDGIVIPDLPLEERERVKEIADRYEFYII 151 ***********9.*********************************************************** PP TIGR00262 145 flvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkel 216 lvaPt+e +r+ ki + ++Gf+Y+vs+ Gvtg+r+ ++++vk+ i v + s++P ++GFGis +e ++++ lcl|NCBI__GCF_000008765.1:NP_349754.1 152 PLVAPTSE-DRIGKIVNGAKGFIYCVSTNGVTGVRNIIANDVKAYIDVVSKASNVPKCIGFGISSPEMAQKM 222 ******98.9************************************************************** PP TIGR00262 217 kelgadgvivGsAlvkiieeklddeekaleeleefvke 254 ke dgvi+GsA++ki+ee + +e++++++ ef+++ lcl|NCBI__GCF_000008765.1:NP_349754.1 223 KEY-CDGVIIGSAVMKIVEEDIP-KEEMIRKVGEFISQ 258 ***.899**************88.8999****999976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (263 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: 7.99 // [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