Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate WP_086508145.1 BZY95_RS01015 DNA alkylation response protein
Query= SwissProt::P33224 (541 letters) >NCBI__GCF_002151265.1:WP_086508145.1 Length = 550 Score = 430 bits (1106), Expect = e-125 Identities = 246/516 (47%), Positives = 315/516 (61%), Gaps = 8/516 (1%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH V NQP +S+L+ D L EA+ RE W LAS+G++ G+ LG AN Sbjct: 12 THEVVNQPDTPGDSDLFAGDLPLREALEREAPAWVRQRLASLGREAGSLHVQALGEQANR 71 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 +PPEL +D GRRLD+VR+HPA+H LM N H +AW+E+ R G AA ++L Sbjct: 72 HPPELALFDRHGRRLDEVRYHPAYHELMHLAIDNGWHAVAWQEEGRGGHQAHIAALYLL- 130 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 Q E G CP+TMT AA P+L + P W LL++ YD LP QKRGL GM M Sbjct: 131 TQAEPGFCCPVTMTHAAMPVLRRS-PDIEAAWAPGLLANAYDPRPLPAEQKRGLTFGMAM 189 Query: 185 TEKQGGSDVMSNTTRAERLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFVPRFL 244 TEKQGGSDV NTTRAER +G +RL GHKWF S P SDA L LAQT GL+CF PRF Sbjct: 190 TEKQGGSDVRRNTTRAERDGEG-WRLTGHKWFCSAPMSDAFLTLAQTDAGLTCFLAPRFT 248 Query: 245 PDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRFDCAL 304 PDG+RNAI L+RLK+K GNR+NAS E+E++ A L+G G G+ I+ M TR D A Sbjct: 249 PDGERNAIELQRLKEKCGNRANASAEIEYRSAWASLVGEPGRGVATIIDMVQQTRLDAAT 308 Query: 305 GSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLARAW-- 362 MMR+A A H RH FG L +QPLM+ V++ +AL++E AL+ R ARA+ Sbjct: 309 APVGMMRQALVEAWRHVRGRHAFGRLLAEQPLMQAVIADLALEVEAGVALVMRAARAFDG 368 Query: 363 DRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPVNS 422 D R +A E AR+ AK+ KRG F+AEAME LGGIGY EE+ L RLYRE PVNS Sbjct: 369 DARGEAHETALARVLPTLAKYWHNKRGPGFMAEAMECLGGIGYVEEAPLARLYREAPVNS 428 Query: 423 IWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPAEEL- 481 IWEGSGN++CLD+LRVL + L + +G + D A+ L+ L PAE L Sbjct: 429 IWEGSGNVICLDLLRVLARHPESIAALRDELRAAQGLQQDLDLALAGLEHDLALPAETLE 488 Query: 482 --GREITHQLFLLGCGAQMLKYASPPMAQAWCQVML 515 R +T +L GA +L++A +A+ +C+ L Sbjct: 489 PRARWLTQRLAQSLQGALLLRHAPAEVAETFCRSRL 524 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: 765 Number of extensions: 28 Number of successful extensions: 5 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: 550 Length adjustment: 35 Effective length of query: 506 Effective length of database: 515 Effective search space: 260590 Effective search space used: 260590 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 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