Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); 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= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1933 Length = 386 Score = 269 bits (687), Expect = 1e-76 Identities = 149/372 (40%), Positives = 220/372 (59%), Gaps = 6/372 (1%) Query: 7 KYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTV 66 ++Q + + F E EV P + +++ E + G + + P+EYGG G D + Sbjct: 10 EHQAFADSFRRFIEKEVTPHHADWEDQGYVAREVWSQAGANGFLCMSLPEEYGGAGADKL 69 Query: 67 GYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTE 126 + +EEL+R GTTG+ H+ + + I YG EEQK+K+L +ASG +GA ++E Sbjct: 70 YSVAQMEELARA-GTTGIGFGLHSEIVAPYILHYGTEEQKRKYLPQMASGAVVGAIAMSE 128 Query: 127 PNAGTDASGQQTTAV--LDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184 P AG+D G +TTA+ DG Y+LNGSK FITN D+ +V+A TD + G KG S + Sbjct: 129 PAAGSDLQGIKTTAIKSADGSHYVLNGSKTFITNGWHADLVIVVAKTDPAAGAKGTSLLL 188 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLG---KEGQGFKIAMSTLDGG 241 VE+G PGF G + KK+G++ TSEL F D ++P ENLLG EG+GF M L Sbjct: 189 VERGMPGFEKGQRLKKLGMKAQDTSELFFNDVKVPAENLLGGPAMEGRGFICLMEQLPWE 248 Query: 242 RIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQA 301 R+ IA A+ AQ A+D T+ YVKER FG+P++ FQNT++ LA+++ +VQ AR V + Sbjct: 249 RLQIAITAVAAAQAAIDWTLDYVKERKVFGQPVASFQNTRYTLAELQTEVQVARVFVDKC 308 Query: 302 AINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIY 361 + A+MAK + + +V + VQ+ GGYGY +YP+ R DA++ IY Sbjct: 309 CELIARDQLDTQTASMAKYWTTDLQCKVMDECVQMFGGYGYMWEYPITRAYADARVQRIY 368 Query: 362 EGTSEVQRMVIS 373 GT+E+ + VIS Sbjct: 369 GGTNEIMKEVIS 380 Lambda K H 0.315 0.133 0.373 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: 352 Number of extensions: 16 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: 378 Length of database: 386 Length adjustment: 30 Effective length of query: 348 Effective length of database: 356 Effective search space: 123888 Effective search space used: 123888 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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