Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate BPHYT_RS18740 BPHYT_RS18740 acyl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__BFirm:BPHYT_RS18740 Length = 561 Score = 462 bits (1189), Expect = e-134 Identities = 257/526 (48%), Positives = 324/526 (61%), Gaps = 16/526 (3%) Query: 4 QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63 QTH V NQ PL + NL+ SD AL A+ R+GAGW L G L T E+L L LAN Sbjct: 8 QTHEVTNQVPPLADYNLFSSDAALSAALERDGAGWHRGALVRHGAALTTPETLALAELAN 67 Query: 64 VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123 + PEL+ + +G R+D + FHP+WH L+ L +H L + + R GA VAR A + L Sbjct: 68 RHEPELVTHSPRGERIDALEFHPSWHALLSLLRREGLHALPFSDPQR-GAMVARCAGYFL 126 Query: 124 HAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMG 183 HAQ+E+GSLCP+TMTFA+ P+L Q PA F L + +DS LP QK +IGMG Sbjct: 127 HAQIESGSLCPLTMTFASIPVL-QREPALFATLRDKLYAREHDSRDLPLKQKTSAMIGMG 185 Query: 184 MTEKQGGSDVMSNTTRAERL----EDGSYRLVGHKWFFSVPQSDAHLVLAQTAG--GLSC 237 MTEKQGGSDV SN TRA +YRLVGHKWFFS PQ DAHLVL +T GLSC Sbjct: 186 MTEKQGGSDVRSNQTRAYSTAGSGRGAAYRLVGHKWFFSAPQCDAHLVLGRTDEHEGLSC 245 Query: 238 FFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGM 297 F+VPRF PDG++N ++++RLKDKLGNRSNAS EVEF DA G ++G EG G+ I++M Sbjct: 246 FYVPRFAPDGRKNNVQIQRLKDKLGNRSNASSEVEFLDAFGIMIGDEGRGVPTIIEMANY 305 Query: 298 TRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFR 357 TR DC +GS A+MR A AI+HA R FG L QPLMR+VL+ +AL+ E T L R Sbjct: 306 TRLDCVIGSAALMRAALVQAIHHARHRSAFGRHLADQPLMRNVLADLALESEAATVLFMR 365 Query: 358 LARAWDRRADA-----KEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELP 412 LARA++ DA E W R+ TPAAK+ +CKR + F EAMEV GG GY E + Sbjct: 366 LARAFEESTDAASTSLAERAWRRIVTPAAKYWVCKRALEFTGEAMEVWGGNGYVETGPMA 425 Query: 413 RLYREMPVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQ 472 R YRE PVNSIWEGSGN+MCLDVLR + ++ L A+ A+ +L Sbjct: 426 RFYREAPVNSIWEGSGNVMCLDVLRAMEREPEAAQALFAAWHADAQAHPALSAALGKLAA 485 Query: 473 QLRKPAEE---LGREITHQLFLLGCGAQMLKYASPPMAQAWCQVML 515 L PAE R I Q+ L+ +LK+A +A+A+ L Sbjct: 486 TLNGPAEHREASARRIAQQVVLIAQATLLLKHAPAEVAEAFVATRL 531 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: 682 Number of extensions: 25 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: 561 Length adjustment: 36 Effective length of query: 505 Effective length of database: 525 Effective search space: 265125 Effective search space used: 265125 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 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