Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_005816735.1 DHAF_RS12300 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000021925.1:WP_005816735.1 Length = 293 Score = 351 bits (901), Expect = e-101 Identities = 169/289 (58%), Positives = 220/289 (76%) Query: 3 EQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIM 62 E+ I+LNGEFV + EAK+SV+DHG+LYGDG+FEGIR Y G +F+ +EHL RLYESAK+IM Sbjct: 2 EKLIYLNGEFVTQAEAKISVFDHGFLYGDGIFEGIRAYHGRIFKCKEHLDRLYESAKTIM 61 Query: 63 LEIPYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSL 122 L I S E+ ++ T+R+N L NGYIRLVVSRG G+LGLDP++C +++ IA+Q+ + Sbjct: 62 LNIGISKGEMEEVLCSTLRKNNLDNGYIRLVVSRGVGDLGLDPNNCVGASIICIADQIKI 121 Query: 123 FPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGY 182 +PQE YE+G+ V TVA RR PD LSP+VKSLNYLNNI+ +IE+ AGV EA+ML +GY Sbjct: 122 YPQEMYEQGLDVKTVAVRRTNPDSLSPRVKSLNYLNNIMAKIESTQAGVVEAIMLTQEGY 181 Query: 183 VAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVAD 242 V EG+ DN+FI++ L+TPP S+G LEG+TRNA++E+ +K G +VREELF RHDVY A+ Sbjct: 182 VVEGTADNIFILRRGALLTPPLSSGCLEGVTRNAVIELAKKRGLEVREELFNRHDVYNAE 241 Query: 243 EVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVIEDGEKI 291 E FLTGTAAE+I V DGR I GQ G LL++FR L + DG I Sbjct: 242 ECFLTGTAAELIPVVKADGRVIAEGQPGEIFKDLLKDFRALTLVDGVPI 290 Lambda K H 0.317 0.138 0.390 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: 309 Number of extensions: 5 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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: 48 (23.1 bits)
Align candidate WP_005816735.1 DHAF_RS12300 (branched-chain-amino-acid transaminase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))
# 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/TIGR01122.hmm # target sequence database: /tmp/gapView.12322.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: branched-chain amino acid aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-102 326.8 0.0 7.1e-102 326.5 0.0 1.0 1 lcl|NCBI__GCF_000021925.1:WP_005816735.1 DHAF_RS12300 branched-chain-amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_005816735.1 DHAF_RS12300 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.5 0.0 7.1e-102 7.1e-102 1 283 [. 6 282 .. 6 289 .. 0.97 Alignments for each domain: == domain 1 score: 326.5 bits; conditional E-value: 7.1e-102 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +l+Ge+v ++ak++v++h+++YG+g+feGiRaY++ +if+ keh++Rly+sak++ l+i +sk e lcl|NCBI__GCF_000021925.1:WP_005816735.1 6 YLNGEFVTQAEAKISVFDHGFLYGDGIFEGIRAYHG----RIFKCKEHLDRLYESAKTIMLNIGISKGE 70 89**********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 + ev +lrknnl++ YiR +v +G++dlgl+p+ + ++i++a ++ y e +e+G++vk++++ lcl|NCBI__GCF_000021925.1:WP_005816735.1 71 MEEVLCSTLRKNNLDNGYIRLVVSRGVGDLGLDPNNCVGASIICIADQIKIYPQ-EMYEQGLDVKTVAV 138 **********************************87778999999999888776.68************ PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr++++s+ +++k+ + Yln+++ak+e+++aG+ eai+L +eGyv+eG+ +nifi++ g+lltPp+s+ lcl|NCBI__GCF_000021925.1:WP_005816735.1 139 RRTNPDSLSPRVKSLN-YLNNIMAKIESTQAGVVEAIMLTQEGYVVEGTADNIFILRRGALLTPPLSSG 206 ***************9.**************************************************** PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+g+tr+avi+lak++g+ev+ee + r+++y a+e fltGtaae++P+++ Dgr i eg+ G++ k l lcl|NCBI__GCF_000021925.1:WP_005816735.1 207 CLEGVTRNAVIELAKKRGLEVREELFNRHDVYNAEECFLTGTAAELIPVVKADGRVIAEGQPGEIFKDL 275 ********************************************************************* PP TIGR01122 277 qeaffdl 283 + f l lcl|NCBI__GCF_000021925.1:WP_005816735.1 276 LKDFRAL 282 **99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (293 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.52 // [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