Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_104486877.1 UN63_RS11415 branched-chain amino acid transaminase
Query= BRENDA::P0AB80 (309 letters) >NCBI__GCF_002936955.1:WP_104486877.1 Length = 307 Score = 431 bits (1108), Expect = e-125 Identities = 197/302 (65%), Positives = 248/302 (82%) Query: 6 ADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSA 65 A YIWFNG+MV WE A+VHVMSHALHYG+SVFEGIR Y++ +GP++FR EH+QRL DSA Sbjct: 4 AKYIWFNGDMVPWEKAQVHVMSHALHYGSSVFEGIRAYETPRGPMIFRLEEHVQRLFDSA 63 Query: 66 KIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAF 125 KIYR + + +ELM+ACR + +N L SAY+RPL+F+G+VGMG+N P DVI+AA Sbjct: 64 KIYRMKIPYTHEELMDACRKAVSENELNSAYLRPLVFIGNVGMGLNAPKDVPCDVIVAAI 123 Query: 126 PWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIA 185 PWGAYLG E LE+G+D V+SWNR APNT+PT AKAGGNYLSS L+ EA+RHGY EGI+ Sbjct: 124 PWGAYLGEEGLERGVDVCVTSWNRLAPNTMPTGAKAGGNYLSSQLISGEAKRHGYDEGIS 183 Query: 186 LDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE 245 LDV+G++SEGAGENLF +K+ VL+TPP T+ LPGITRD ++ LA+E G +VRE+ +SRE Sbjct: 184 LDVHGHLSEGAGENLFLIKNKVLYTPPVTACILPGITRDTLMTLAREAGYQVREEAISRE 243 Query: 246 SLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLD 305 +LYLADE+FM+GTAAE+TPVRSVDGI++G G+ GP+T +Q+AFFGLF G T DKWGWL Sbjct: 244 ALYLADEMFMTGTAAEVTPVRSVDGIELGAGKRGPITTELQKAFFGLFDGSTRDKWGWLT 303 Query: 306 QV 307 V Sbjct: 304 PV 305 Lambda K H 0.319 0.136 0.413 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: 365 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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_104486877.1 UN63_RS11415 (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.carbon/TIGR01122.hmm # target sequence database: /tmp/gapView.3170514.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-139 449.1 0.0 3.8e-139 448.9 0.0 1.0 1 NCBI__GCF_002936955.1:WP_104486877.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002936955.1:WP_104486877.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.9 0.0 3.8e-139 3.8e-139 1 298 [] 8 305 .. 8 305 .. 1.00 Alignments for each domain: == domain 1 score: 448.9 bits; conditional E-value: 3.8e-139 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 w++G++v++e a+vhv++halhYG++vfeGiRaYet++g++ifrl+ehv+Rl+dsaki+r++ipy++eel+++ NCBI__GCF_002936955.1:WP_104486877.1 8 WFNGDMVPWEKAQVHVMSHALHYGSSVFEGIRAYETPRGPMIFRLEEHVQRLFDSAKIYRMKIPYTHEELMDA 80 9************************************************************************ PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 +++++ +n+l+saY+Rplv++G+ ++gl+++ d++ +vi+aa++wgaylgee+le+G++v v+s++r a+n++ NCBI__GCF_002936955.1:WP_104486877.1 81 CRKAVSENELNSAYLRPLVFIGNVGMGLNAPKDVPCDVIVAAIPWGAYLGEEGLERGVDVCVTSWNRLAPNTM 153 ************************************************************************* PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 pt aka+gnYl+s+l+ ea+r+Gyde+i Ld +G+++eG+Gen+f++k+ vl+tPpv+ iL gitrd++++ NCBI__GCF_002936955.1:WP_104486877.1 154 PTGAKAGGNYLSSQLISGEAKRHGYDEGISLDVHGHLSEGAGENLFLIKNKVLYTPPVTACILPGITRDTLMT 226 ************************************************************************* PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292 la+e g++v+ee isre+ly+aDe+f+tGtaaevtP+r+vDg+++g+gkrGp+t +lq+aff l+ g t++k+ NCBI__GCF_002936955.1:WP_104486877.1 227 LAREAGYQVREEAISREALYLADEMFMTGTAAEVTPVRSVDGIELGAGKRGPITTELQKAFFGLFDGSTRDKW 299 ************************************************************************* PP TIGR01122 293 ewltyv 298 +wlt+v NCBI__GCF_002936955.1:WP_104486877.1 300 GWLTPV 305 ***987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 24.94 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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