Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate Ac3H11_1933 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1933 Length = 386 Score = 257 bits (657), Expect = 3e-73 Identities = 144/375 (38%), Positives = 213/375 (56%), Gaps = 6/375 (1%) Query: 6 DQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGYL 65 + Q D R F ++ + P A+W+ + +E + GF M +PE++GG L Sbjct: 10 EHQAFADSFRRFIEKEVTPHHADWEDQGYVAREVWSQAGANGFLCMSLPEEYGGAGADKL 69 Query: 66 AYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALTE 125 +EE+A G +H+ + IL+YGT+EQK ++L +ASGA++GA A++E Sbjct: 70 YSVAQMEELARA-GTTGIGFGLHSEIVAPYILHYGTEEQKRKYLPQMASGAVVGAIAMSE 128 Query: 126 PQAGSDASGLKTRA--RLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 P AGSD G+KT A +G HYVLNG K FIT+G +A +VIV A TDP+AG +G S + Sbjct: 129 PAAGSDLQGIKTTAIKSADGSHYVLNGSKTFITNGWHADLVIVVAKTDPAAGAKGTSLLL 188 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGE---EGEGYRIALANLEGG 240 V PG++ + KLG A DT ++ F DVKVP N LG EG G+ + L Sbjct: 189 VERGMPGFEKGQRLKKLGMKAQDTSELFFNDVKVPAENLLGGPAMEGRGFICLMEQLPWE 248 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+ IA +V A+AA + DY +ER+ FG+P+ Q + LA++ T++ VAR V Sbjct: 249 RLQIAITAVAAAQAAIDWTLDYVKERKVFGQPVASFQNTRYTLAELQTEVQVARVFVDKC 308 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIY 360 L + ASMAK + +++ KV +Q GGYGY+ ++P+ R Y D RV +IY Sbjct: 309 CELIARDQLDTQTASMAKYWTTDLQCKVMDECVQMFGGYGYMWEYPITRAYADARVQRIY 368 Query: 361 EGTSDIQRMVISRNL 375 GT++I + VISR + Sbjct: 369 GGTNEIMKEVISRGM 383 Lambda K H 0.320 0.135 0.394 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: 362 Number of extensions: 16 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: 375 Length of database: 386 Length adjustment: 30 Effective length of query: 345 Effective length of database: 356 Effective search space: 122820 Effective search space used: 122820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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