Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate HSERO_RS04905 HSERO_RS04905 acyl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__HerbieS:HSERO_RS04905 Length = 550 Score = 476 bits (1224), Expect = e-138 Identities = 269/525 (51%), Positives = 330/525 (62%), Gaps = 11/525 (2%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH + NQ L+ NLY SD AL EAV REGA W LAS G+ LG AE E+ LAN Sbjct: 3 THEITNQVPDLSGYNLYRSDAALAEAVQREGAHWHDCTLASQGELLGGAEMREMAELANR 62 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 + P L +D GRR+D V FHPAWH L+ L +H L W + GA ARAA + LH Sbjct: 63 HTPVLHTHDRCGRRIDVVEFHPAWHTLLDQLRRAGLHALPWMQPG-DGAHAARAAGYFLH 121 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 AQ+EAGSLCP TMTFAA +L Q PA F+ T L S +D+ LP QKR +LIGMGM Sbjct: 122 AQIEAGSLCPTTMTFAAIAVL-QQEPALFEQLRTRLFSREHDARDLPIPQKRSILIGMGM 180 Query: 185 TEKQGGSDVMSNTTRA---ERLEDG---SYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCF 238 TEKQGGSDV SN + A + L DG +Y L GHKWFFS P DAHL+LA+T GLSCF Sbjct: 181 TEKQGGSDVRSNASIAMPVDPLNDGRGAAYLLSGHKWFFSAPMCDAHLMLARTENGLSCF 240 Query: 239 FVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMT 298 FVPR+LPDG RN I ++RLKDKLGNRSN+S EVEF++A+G ++G EG GI I++M T Sbjct: 241 FVPRWLPDGTRNPILIQRLKDKLGNRSNSSSEVEFEEAMGIMVGDEGRGIPTIIEMANHT 300 Query: 299 RFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRL 358 R DC +GS A+MR+A AI+HA R FG L +QPLMR VL+ +AL+ E T L+ R+ Sbjct: 301 RLDCIIGSAALMRQALVQAIHHARHRSAFGRRLAEQPLMRAVLADLALESEAATMLMLRV 360 Query: 359 ARAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREM 418 A A+D D + W R+ TPAAKF ICKR + F E MEV GG GY E + + RLYRE Sbjct: 361 AHAFDAPDDPLQRAWKRIITPAAKFWICKRTLEFTGECMEVWGGNGYVETAPMARLYREA 420 Query: 419 PVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPA 478 PVNSIWEGSGN+MCLDVLR + ++ LL + + V L+Q L P Sbjct: 421 PVNSIWEGSGNVMCLDVLRAMARETQGLALLLLELDDAAAGHPALRQQVDALKQMLAAPE 480 Query: 479 EEL---GREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGG 520 EE R + QL L G ML++A AQA+ + GG Sbjct: 481 EEREAGARRLVQQLVLALQGMLMLRHAPAGSAQAFLESRSQADGG 525 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: 745 Number of extensions: 32 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 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