Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate RR42_RS01285 RR42_RS01285 acyl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__Cup4G11:RR42_RS01285 Length = 553 Score = 417 bits (1071), Expect = e-121 Identities = 243/527 (46%), Positives = 310/527 (58%), Gaps = 13/527 (2%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH VFNQ L NL+ D AL A+ R G GW + L G +LG + + AN Sbjct: 6 THRVFNQVPDLTGYNLFTGDPALRAALERLGGGWHASALDIFGARLGKPDVQQWAAEANR 65 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 + PEL + G R+D+V F PAWH L+ L + ++ L + + R GA+VARAA + L Sbjct: 66 HAPELHTHSRTGERIDEVEFPPAWHALLALLRSQQLQALPFAQP-REGAWVARAAGYFLQ 124 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 AQ E+GSLCP TMTFA+ P+L Q F + L + +D LP K ++IGMGM Sbjct: 125 AQAESGSLCPPTMTFASIPVL-QKEATLFAELGPKLFATLHDPRDLPWRDKHAVMIGMGM 183 Query: 185 TEKQGGSDVMSNTTRAERLEDGS----YRLVGHKWFFSVPQSDAHLVLAQTA---GGLSC 237 TEKQGGSDV SNTT A + G Y + GHKWFFS P DAH+V+A+ G LSC Sbjct: 184 TEKQGGSDVRSNTTVARAVRGGGRGAEYAITGHKWFFSAPMCDAHMVVARMGAQDGPLSC 243 Query: 238 FFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGM 297 FFVPRF DG +N ++++RLKDKLGNRSNAS EVEF++A G L+G EG GI I++M Sbjct: 244 FFVPRFRDDGSKNPVQIQRLKDKLGNRSNASSEVEFREATGILIGEEGRGIPTIIEMATY 303 Query: 298 TRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFR 357 TR DC +GS A++R A AI+HA R FG L++QPLMR+VL+ +AL+ + T L+ Sbjct: 304 TRLDCVIGSAAIIRAALVQAIHHARHRMAFGRLLVEQPLMRNVLADLALESQAATLLMME 363 Query: 358 LARAWDRR-ADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYR 416 LA A++R AD A W R+ TPAAKF +CKR + EAMEV GG GY EE + RLYR Sbjct: 364 LAHAFERADADPLAAAWKRIVTPAAKFWVCKRAIEVTGEAMEVWGGNGYVEEGPMARLYR 423 Query: 417 EMPVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRK 476 E PVNSIWEGSGNIMCLDVLR L + L + G A+ LQ LR Sbjct: 424 EAPVNSIWEGSGNIMCLDVLRALQRNPEDAGRLLQDLSRRAGGHPAVRAALASLQAMLRD 483 Query: 477 PAEEL---GREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGG 520 + L R L L A ML +A A+ + L + G Sbjct: 484 APDLLEAGARRFAQGLVLTAQAALMLAHADADDAERFVASRLGHQHG 530 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: 748 Number of extensions: 41 Number of successful extensions: 6 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: 553 Length adjustment: 36 Effective length of query: 505 Effective length of database: 517 Effective search space: 261085 Effective search space used: 261085 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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