Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate Ac3H11_2514 Acyl-CoA dehydrogenase (EC 1.3.8.7)
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2514 Length = 553 Score = 422 bits (1085), Expect = e-122 Identities = 243/543 (44%), Positives = 323/543 (59%), Gaps = 18/543 (3%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH VFNQ P + NL+ ++ L +A+ G LA++G ++G+AE RLAN Sbjct: 9 THEVFNQSTPWADVNLFTTNQPLQDALRLHAPGLPLAGLAALGAEMGSAEMQAHARLANT 68 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 P+L +D G R D V FHP++H L+ A + +H W A + RAA FML Sbjct: 69 YKPQLRTHDRFGHRTDVVEFHPSYHALIGAALRHGLHATPWSRQDTGHAHIERAAGFMLF 128 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 + E LCP++M++A TP L + A + DW+ L S +YD L QK L +GMGM Sbjct: 129 TEAEPSVLCPVSMSYAVTPAL-RGNAAVWADWSKGLASTQYDPRLALFSQKSALTMGMGM 187 Query: 185 TEKQGGSDVMSNTTRAERLEDGS------YRLVGHKWFFSVPQSDAHLVLAQTAGGLSCF 238 TEKQGGSDV +NTT+A + DG YR++GHKWFFS P DA L+LAQ GGL+CF Sbjct: 188 TEKQGGSDVRANTTQA--VPDGEDAWGARYRIIGHKWFFSAPMCDAFLILAQAPGGLTCF 245 Query: 239 FVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMT 298 F+PR LPD NAIR++RLKDKLGN +NAS EVEF A W +G EG G+ IL+MG MT Sbjct: 246 FLPRVLPDDTVNAIRIQRLKDKLGNHANASSEVEFIGATAWRVGEEGRGVAQILEMGTMT 305 Query: 299 RFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRL 358 R DCALG+ +MR+A S+A++H QR FG LI QPLMR+VL+ +AL+ E TAL RL Sbjct: 306 RLDCALGTSGLMRQALSIALHHTRQRSAFGKKLIDQPLMRNVLADLALESEAATALSIRL 365 Query: 359 ARAWDRRADAK-EALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCE---ESELPRL 414 A A+D + ++ EA+ ARL TP AKF +CKRG F EAME LGG GY E E + R+ Sbjct: 366 ASAFDHKDKSEHEAVMARLLTPVAKFWVCKRGSVFAQEAMECLGGNGYVEEGGEGTMARI 425 Query: 415 YREMPVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQL 474 YREMP+NSIWEG+GNIM LD+LR + ++A L++ +G DR L ++ Sbjct: 426 YREMPLNSIWEGAGNIMALDLLRAV-RRADTAAALADELAPARGAHPALDRMASALPLRV 484 Query: 475 -RKPAEELGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGGV---RLSEQIQND 530 E R + + L A + + A + A+C L G L ++ D Sbjct: 485 DAMTTEAEARRLAQDVALAVQAALLYRSAPSAVFSAFCDSRLGGDWGYSFGTLGAGVEFD 544 Query: 531 LLL 533 LLL Sbjct: 545 LLL 547 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: 710 Number of extensions: 26 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: 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