Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate N515DRAFT_0941 N515DRAFT_0941 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Dyella79:N515DRAFT_0941 Length = 385 Score = 249 bits (636), Expect = 9e-71 Identities = 129/368 (35%), Positives = 218/368 (59%), Gaps = 2/368 (0%) Query: 10 ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 + ++ FA++ + P A + D ++ FP + + E+G GM +PE +GG GYLA+ + Sbjct: 13 LRESVHAFAEKEIAPRATQIDHDNVFPADLWRKFGEMGLLGMTIPEAYGGTGLGYLAHMV 72 Query: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129 A+EEI+ G+ H+++ + GN++Q+ +++ L SG +GA A++EP AG Sbjct: 73 AMEEISRASGSVGLSYGAHSNLCVQNLFHNGNEEQRRKYIPRLCSGEYVGALAMSEPGAG 132 Query: 130 SDA-SSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPS-AGKRGISAFIVPTD 187 SD S+ +A L GD +V NG K +IT+G +A V++V+ T P AG R ++AFI+ Sbjct: 133 SDVVGSMSCKAELRGDVWVANGTKMWITNGPDADVLLVYMRTAPRPAGSRCMTAFIIEKG 192 Query: 188 SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQ 247 G+ A+ DKLG S+TC+++FED ++P AN +GE EG ++ ++ L+ R+ ++ Sbjct: 193 MKGFSTAQKLDKLGMRGSNTCELVFEDCEIPAANIVGEVNEGVRVLMSGLDTERLVLSGG 252 Query: 248 SVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSG 307 +G+ +AA + Y RER+ F PI + ++ADM T + +R + A D G Sbjct: 253 PLGLMQAAMDLVLPYVRERKQFNAPIGTFGMMQAKVADMYTALQSSRGFAYMVAREFDQG 312 Query: 308 KPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQ 367 + ++ + L AS+ A KV A+Q LGG GY+++FP R+ RD ++ +I GT++I+ Sbjct: 313 SKSRIDPAACLLNASQNAVKVALEAIQALGGNGYINEFPAGRLLRDAKLYEIGAGTNEIR 372 Query: 368 RMVISRNL 375 RM+I R L Sbjct: 373 RMLIGREL 380 Lambda K H 0.319 0.134 0.389 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: 320 Number of extensions: 17 Number of successful extensions: 3 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: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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