Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate WP_156966386.1 U743_RS08760 DNA alkylation response protein
Query= SwissProt::P33224 (541 letters) >NCBI__GCF_000733765.1:WP_156966386.1 Length = 560 Score = 404 bits (1037), Expect = e-117 Identities = 219/513 (42%), Positives = 305/513 (59%), Gaps = 9/513 (1%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH V NQP PL + N + D AL EAV REG W + L + G + G+ E + G AN Sbjct: 16 THEVTNQPPPLQDYNAFEGDTALVEAVKREGGAWGIEALRADGARTGSEEVISWGYRANA 75 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 PEL +D QG R+D V +H +H LM +H+ W D + GA V R+A +H Sbjct: 76 YKPELQAFDRQGHRIDQVAYHEDYHRLMAHSLQAGIHSSPWA-DPKPGAHVVRSALQYMH 134 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 QV+AG CP+TMTFA P + + P+ + W +L+ YD +P QKR L +GMGM Sbjct: 135 YQVDAGHHCPVTMTFACVPAI-RTTPSVAEQWLPGILTADYDPRDIPHTQKRALTVGMGM 193 Query: 185 TEKQGGSDVMSNTTRAERLEDGS-----YRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFF 239 TEKQGGSDV NTT A + +G+ Y L+GHKWF S P DA L+LAQT GGLSCF Sbjct: 194 TEKQGGSDVRINTTSARPVGNGTGPGAVYELLGHKWFTSAPMCDAFLMLAQTEGGLSCFL 253 Query: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTR 299 VPR+ DG +N I+++RLK+K GN SNAS E+E + A G +LG EG G+ I++M MTR Sbjct: 254 VPRWREDGSKNPIQVQRLKNKAGNVSNASSEIELRGAQGRMLGEEGRGVPTIIEMVAMTR 313 Query: 300 FDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLA 359 +DC +GS A MR+A + AI+H R FG LI+QP M +VL+ + L++EG AL R+ Sbjct: 314 YDCMVGSTASMRQATAQAIHHCAHREAFGKRLIEQPAMANVLADLQLEVEGALALTMRMG 373 Query: 360 RAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMP 419 RA D D E L RL P K+ ICKR EAME +GG G ++ + RLYR+ P Sbjct: 374 RALDNPDDEHEKLLLRLGLPTGKYWICKRNPNHTYEAMECIGGNGVMDDFIMARLYRDAP 433 Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQL--RKP 477 +N+IWEGSGN+ LD+LR ++K ++ +G +FD A+ L L ++ Sbjct: 434 INAIWEGSGNVQALDLLRAMSKSPAALEVFLGELEAARGMHDHFDAALDHLHAALSDQEA 493 Query: 478 AEELGREITHQLFLLGCGAQMLKYASPPMAQAW 510 E R++ ++ L + +L++ + +A+A+ Sbjct: 494 LEHRARDLAERMALCMQASLLLRHGNARVAEAF 526 Lambda K H 0.324 0.138 0.428 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: 703 Number of extensions: 29 Number of successful extensions: 4 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: 541 Length of database: 560 Length adjustment: 36 Effective length of query: 505 Effective length of database: 524 Effective search space: 264620 Effective search space used: 264620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 bits)
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