Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_041941002.1 FRAAL_RS25445 branched-chain-amino-acid transaminase
Query= metacyc::MONOMER-11914 (306 letters) >NCBI__GCF_000058485.1:WP_041941002.1 Length = 308 Score = 322 bits (826), Expect = 5e-93 Identities = 154/302 (50%), Positives = 213/302 (70%) Query: 1 MSCEASGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKR 60 M + KIW++GE+V+W++A +HVL+ +HYG VFEGIRCY ++G A+FRL +H+ R Sbjct: 1 MPITPTSKIWMSGELVDWDDARIHVLNPTLHYGWGVFEGIRCYETAEGPAVFRLSDHIAR 60 Query: 61 LFDSAKIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGEMGVHPVNCPVDVA 120 L+ SAKIY M+ +TQE++ A ET+ N + CYIRP+V+ GYGEMG++P+ PV+V Sbjct: 61 LYRSAKIYVMEPSFTQEEVVAATKETIAVNDISSCYIRPLVYLGYGEMGLNPLPSPVEVM 120 Query: 121 VAAWEWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYD 180 +A W WGAYLG EA GV A +S+W+R PN P AKA G YLNS LAK+ AV+ GYD Sbjct: 121 IAVWPWGAYLGEEAEANGVRAQISSWKRNDPNITPPAAKASGQYLNSSLAKVAAVKAGYD 180 Query: 181 EAIMLDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEP 240 EAI+ +G+I++G+GEN+F+VS ++ TP ++ L GITR S+++IA +G V E+ Sbjct: 181 EAILTSPNGHIADGTGENVFIVSGRQVITPLLTDGPLGGITRASIMQIAADQGYEVVEQH 240 Query: 241 ITREMLYIADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSF 300 + R LY+ADEAFFTGTAAEI PI SVD ++GAG+ GPVT+ L + F R R E + Sbjct: 241 VVRTDLYLADEAFFTGTAAEIVPIVSVDDRQVGAGKPGPVTRELLEIFHRATRGELDRYR 300 Query: 301 GW 302 W Sbjct: 301 SW 302 Lambda K H 0.320 0.136 0.414 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: 337 Number of extensions: 9 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: 306 Length of database: 308 Length adjustment: 27 Effective length of query: 279 Effective length of database: 281 Effective search space: 78399 Effective search space used: 78399 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: 48 (23.1 bits)
Align candidate WP_041941002.1 FRAAL_RS25445 (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.25073.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-125 403.4 0.0 3.1e-125 403.2 0.0 1.0 1 lcl|NCBI__GCF_000058485.1:WP_041941002.1 FRAAL_RS25445 branched-chain-ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_041941002.1 FRAAL_RS25445 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.2 0.0 3.1e-125 3.1e-125 1 297 [. 10 305 .. 10 306 .. 0.99 Alignments for each domain: == domain 1 score: 403.2 bits; conditional E-value: 3.1e-125 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+ Gelvd++da++hvl+ +lhYG gvfeGiR+Yet +g+a+frl++h+ Rly saki+ +e ++++ee lcl|NCBI__GCF_000058485.1:WP_041941002.1 10 WMSGELVDWDDARIHVLNPTLHYGWGVFEGIRCYETAEGPAVFRLSDHIARLYRSAKIYVMEPSFTQEE 78 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 +v +tke++ +n+++s+YiRplvy+G++++gl+p +vev+ia+w+wgaylgeea +G+++++ss+ lcl|NCBI__GCF_000058485.1:WP_041941002.1 79 VVAATKETIAVNDISSCYIRPLVYLGYGEMGLNP-LPSPVEVMIAVWPWGAYLGEEAEANGVRAQISSW 146 **********************************.999******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r+++n+ p++aka+g+Ylns lak+ a++aGydeail + +G++a+G+Gen+fiv+ +++tP +++ lcl|NCBI__GCF_000058485.1:WP_041941002.1 147 KRNDPNITPPAAKASGQYLNSSLAKVAAVKAGYDEAILTSPNGHIADGTGENVFIVSGRQVITPLLTDG 215 ********************************************************************* PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 L gitr +++++a+++g+ev+e+++ r++ly+aDe+f+tGtaae++Pi++vD+r++g+gk Gpvt++l lcl|NCBI__GCF_000058485.1:WP_041941002.1 216 PLGGITRASIMQIAADQGYEVVEQHVVRTDLYLADEAFFTGTAAEIVPIVSVDDRQVGAGKPGPVTREL 284 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewlty 297 e f + ++g+ +++ +w + lcl|NCBI__GCF_000058485.1:WP_041941002.1 285 LEIFHRATRGELDRYRSWNEL 305 ******************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (308 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: 00:00:00.01 # Mc/sec: 8.86 // [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