Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate AO353_10705 AO353_10705 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10705 Length = 270 Score = 224 bits (571), Expect = 2e-63 Identities = 123/271 (45%), Positives = 168/271 (61%), Gaps = 9/271 (3%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSR+ + F+ L+ Q R AL+ +VTAG P D + A++ G+ AGADVIELG+PF+DPMAD Sbjct: 1 MSRLQTRFAELKEQNRAALVTFVTAGDPSYDTSLAILKGLPAAGADVIELGMPFTDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GP IQ A +AL + + L VREFRK NN TP+VLMGY NP+ Y G F+ Sbjct: 61 GPAIQLANIRALGAKQNLAKTLQMVREFRKDNNHTPLVLMGYFNPIHYY----GVPRFIS 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 D+ AGVDG+++VD PPE +A G+D I L PT+ D R+ V +SG+VYY Sbjct: 117 DAKEAGVDGLIVVDMPPEHNAELCDPAQAAGIDFIRLTTPTTDDVRLPTVLNGSSGFVYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VS+ GVTG+GA VE+ + R+R+H +P+ +GFGIR A +I ++AD VV+GS + Sbjct: 177 VSVAGVTGAGAATLEHVEEAVARLRRHTDLPISIGFGIRTPEQAASIARLADGVVVGSAL 236 Query: 241 IQLI-----EDQEHAKVVPLTIDFLRGIRKA 266 I I +Q V+ L G+RKA Sbjct: 237 IDHIANATTPEQAIDGVLGLCSALSEGVRKA 267 Lambda K H 0.321 0.137 0.389 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: 249 Number of extensions: 10 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: 269 Length of database: 270 Length adjustment: 25 Effective length of query: 244 Effective length of database: 245 Effective search space: 59780 Effective search space used: 59780 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate AO353_10705 AO353_10705 (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.28520.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-81 258.2 0.0 3e-81 258.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_10705 AO353_10705 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_10705 AO353_10705 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.0 0.0 3e-81 3e-81 1 254 [. 8 259 .. 8 261 .. 0.97 Alignments for each domain: == domain 1 score: 258.0 bits; conditional E-value: 3e-81 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAl 65 f++lk+++ a+v+FvtagdP++++sl i+k l aGad++ElG+pf DP+aDGp+iq a+ RAl lcl|FitnessBrowser__pseudo3_N2E3:AO353_10705 8 FAELKEQNRAALVTFVTAGDPSYDTSLAILKGLPAAGADVIELGMPFTDPMADGPAIQLANIRAL 72 7899************************************************************* PP TIGR00262 66 kagvkvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleead 130 a +++k+l++++++r+++++ P+vl+ y+n+i+++gv F++ akeagvdg++v+D+P e ++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_10705 73 GAKQNLAKTLQMVREFRKDNNHTPLVLMGYFNPIHYYGVPRFISDAKEAGVDGLIVVDMPPEHNA 137 ***************************************************************** PP TIGR00262 131 dlleaakkhgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvka 195 +l + a+ g++ i l +Pt+++ rl ++ + s+GfvY vsvaGvtga e+v+e+++++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_10705 138 ELCDPAQAAGIDFIRLTTPTTDDVRLPTVLNGSSGFVYYVSVAGVTGAGAATLEHVEEAVARLRR 202 ***************************************************************** PP TIGR00262 196 lskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvke 254 +++ P+ +GFGi +eq+ ++ l adgv+vGsAl++ i++ ++e+a++ + ++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_10705 203 HTDLPISIGFGIRTPEQAASIARL-ADGVVVGSALIDHIANA-TTPEQAIDGVLGLCSA 259 ***********************9.9*************998.6799988877766665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (270 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: 9.62 // [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