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_0492 N515DRAFT_0492 hypothetical protein
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 338 bits (867), Expect = 1e-97 Identities = 180/376 (47%), Positives = 253/376 (67%), Gaps = 7/376 (1%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T++QL I AR FAQ+R+ P AAE D + FP E I EM +LG G+ VP ++GG Sbjct: 6 TEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYGGAGMD 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 +AY +A+ EIAA D A ST+MSV+NS+ C ILK GN++QK+++++ +A G +GA+AL Sbjct: 66 PIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAIGAYAL 125 Query: 124 TEPQAGSDASSLKTRARLNGD-HYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAF 182 TEPQ+GSDAS++ TRA N D +V+NG K +ITSG A +++FA++ P G RG+SAF Sbjct: 126 TEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGARGVSAF 185 Query: 183 IVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRV 242 I+ T PG+ + E KLG AS TC+I F D P N LGEEG+G+ IA+ L+ GR+ Sbjct: 186 IIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVLDAGRI 245 Query: 243 GIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAA- 301 GIASQSVG+ARAA+EA ++R+R++FG+ I Q ++ADM ++ A + AA Sbjct: 246 GIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLTLRAAW 305 Query: 302 ----ALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVC 357 A ++ G+ EAS+AKL ASE A + A+Q GG GY + PLER +RD ++ Sbjct: 306 TKGQAEKNGGRFG-TEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRDAKIT 364 Query: 358 QIYEGTSDIQRMVISR 373 +IYEGTS+IQR+VI+R Sbjct: 365 EIYEGTSEIQRLVIAR 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: 341 Number of extensions: 11 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: 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