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 SMa1400 SMa1400 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Smeli:SMa1400 Length = 380 Score = 300 bits (769), Expect = 3e-86 Identities = 170/372 (45%), Positives = 234/372 (62%), Gaps = 10/372 (2%) Query: 11 LKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIM 70 ++++ +FA+ ++P+A LD EERFP E +MAK G+ GI P+ GG G DT+ Y + Sbjct: 10 VRDMARAFADEVIRPMAESLDREERFPAELYGEMAKLGLFGIGVPEHLGGPGFDTLTYAV 69 Query: 71 AVEELSR----VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTE 126 +EELSR V G++ L S + ++G E Q++ L K+ A+ +TE Sbjct: 70 VMEELSRGYASVADQCGLV-----ELISTLLVRHGTEGQQRMLPDVLNMSAKV-AYCITE 123 Query: 127 PNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVE 186 P AGTD SG +TTA DGD ++LNG KI+I NA D+ V+A TDK GN+G+S FIV+ Sbjct: 124 PEAGTDVSGIRTTAERDGDGWMLNGGKIWIHNAPVADVGFVLARTDKEAGNRGMSIFIVD 183 Query: 187 KGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIA 246 + G G KE KMG R S L F D R+P LLG+EG+GF + MS LD GR+GIA Sbjct: 184 LNSAGVERGPKEHKMGQRASQVGALTFTDVRLPGGALLGQEGRGFHMMMSVLDKGRVGIA 243 Query: 247 AQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKD 306 A A+G+AQ L+ V Y R QFG+ +S FQ Q+ LADM ++AAR LV+ AA D Sbjct: 244 ALAVGIAQAGLEAAVDYAGTRKQFGKAISDFQGVQWLLADMAKDIEAARLLVHSAASKID 303 Query: 307 LGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSE 366 G ++AK FA + A++ T AVQ+ GG GY R + VER+ RDAKIT+IYEGT++ Sbjct: 304 RGLDATKACSIAKCFAGDMAVQRTADAVQVFGGSGYIRGFEVERLYRDAKITQIYEGTNQ 363 Query: 367 VQRMVISGKLLK 378 +QRM+I+ +LLK Sbjct: 364 IQRMIIARELLK 375 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: 350 Number of extensions: 16 Number of successful extensions: 2 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: 380 Length adjustment: 30 Effective length of query: 348 Effective length of database: 350 Effective search space: 121800 Effective search space used: 121800 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