Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate SMc01359 SMc01359 oxidoreductase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__Smeli:SMc01359 Length = 550 Score = 411 bits (1057), Expect = e-119 Identities = 231/509 (45%), Positives = 303/509 (59%), Gaps = 5/509 (0%) Query: 10 NQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANVNPPEL 69 NQP P + N + SD + + +T D +G+ + + E+ EL R+AN P+L Sbjct: 15 NQPKPWSGVNAFRSDPLVVD-ITSSMPKTLRDEFDGLGRYVTSPEAQELARMANEGVPKL 73 Query: 70 LRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEE--DARSGAFVARAARFMLHAQV 127 + +G RLD V FHPAWH LM+ T +H+ AWE D R + RA RF L AQ+ Sbjct: 74 KTHGPRGERLDVVEFHPAWHALMRRSMTTGLHSSAWENLPDERGRSHKVRAIRFYLTAQL 133 Query: 128 EAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGMTEK 187 E G LCP+TMT A+ + PA ++W +LS +YDS P QK + IGMGMTEK Sbjct: 134 ECGHLCPLTMTSASVAAITAS-PAVQKEWAPKILSRKYDSSNRPWMQKSAVTIGMGMTEK 192 Query: 188 QGGSDVMSNTTRAERLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFVPRFLPDG 247 QGG+DV +NT+ AER+ +G YRL GHKWF S P SDA ++LAQT GL CF VPR L DG Sbjct: 193 QGGTDVRANTSTAERVGEGIYRLTGHKWFMSAPMSDAFVMLAQTREGLGCFLVPRLLEDG 252 Query: 248 QRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRFDCALGSH 307 N +R +RLKDKLGNRSNAS EVEF D G+LLG GIR IL M +TR DCAL S Sbjct: 253 GANGLRFQRLKDKLGNRSNASSEVEFSDTFGFLLGTPDAGIRTILDMVTLTRLDCALASA 312 Query: 308 AMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLARAWDR-RA 366 MMR + + A++H R VFG L+ QP+M VL+ MAL + +AL FRLA A+D + Sbjct: 313 GMMRASLAEAVHHTRGRKVFGKALVSQPMMTRVLADMALDVAAASALSFRLAEAFDNAHS 372 Query: 367 DAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPVNSIWEG 426 A++A +AR+ TP AK+ CK + EAME +GG GY EE L R YRE PVN+IWEG Sbjct: 373 SAEDAAYARIMTPVAKYWCCKIAPALIYEAMECMGGNGYVEERALARHYREAPVNAIWEG 432 Query: 427 SGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPAEELGREIT 486 SGN+M LDVLRVL ++ +++ L G V R L + E R + Sbjct: 433 SGNVMALDVLRVLGRRKELFEQLFATIGRDLGPAGRKTIEVLRAAMSLCERDEGAARMLV 492 Query: 487 HQLFLLGCGAQMLKYASPPMAQAWCQVML 515 QL L A++ + + +A A+ + L Sbjct: 493 EQLALAAAAAELYRLGAGRIADAFLESRL 521 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: 685 Number of extensions: 26 Number of successful extensions: 4 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