Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_013258106.1 DEBA_RS06410 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000143965.1:WP_013258106.1 Length = 385 Score = 378 bits (971), Expect = e-109 Identities = 191/372 (51%), Positives = 260/372 (69%) Query: 4 NDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTG 63 N++Q+ I+ MARDFA+E L P A + DRE RFP + + MA LGF GM+VPE++GG Sbjct: 7 NEEQRMIQTMARDFAREVLLPGAGQRDREGRFPADMLARMAELGFLGMMVPEEYGGAGVD 66 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFAL 123 ++Y +AL EIA G + + +MSVHNS+ C ++ +G++EQK ++L P+ G ++GAF L Sbjct: 67 AVSYVLALAEIAYGCASTAVVMSVHNSICCEAMVKFGSEEQKRQWLPPMCDGRVIGAFGL 126 Query: 124 TEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSD SG T A +GD++VL+G KQFIT+G NAG+ IV A TD S RG+SAF+ Sbjct: 127 TEPGAGSDPSGQITTAVRDGDYWVLSGVKQFITTGSNAGLTIVTAYTDKSKKHRGVSAFL 186 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVG 243 VP SPG V + EDKLG ASDT Q++ ED +VP AN LG EGEG+R+A+ L+ GR+G Sbjct: 187 VPKGSPGLVVGKAEDKLGLKASDTVQLILEDCRVPAANMLGREGEGFRVAMTCLDAGRIG 246 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA+QS+G+ARA + A + RE FG+ I + Q V +R+ADMAT+I A + AA L Sbjct: 247 IAAQSLGVARACLDEAVTFIDSREQFGRAISQFQGVRWRIADMATEIEAAELLCVNAALL 306 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGT 363 + G+ EASMAKLFASEM ++ S LQ GGYG+ ++ +ER +RD RV IYEGT Sbjct: 307 KAQGQRFTAEASMAKLFASEMVNRITSQCLQLHGGYGFCKEYDIERHFRDARVFTIYEGT 366 Query: 364 SDIQRMVISRNL 375 S+IQR+VIS ++ Sbjct: 367 SEIQRVVISNHV 378 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: 354 Number of extensions: 13 Number of successful extensions: 1 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 24 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