Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_028315572.1 G491_RS0117975 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000429905.1:WP_028315572.1 Length = 379 Score = 392 bits (1008), Expect = e-114 Identities = 203/370 (54%), Positives = 264/370 (71%) Query: 6 DQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGYL 65 +Q+ +R M R+FA+ L P AAE DR FP E + EMA LG GM+VP ++ G + Sbjct: 8 EQKMVRKMVREFARGELMPTAAERDRTKEFPAENLKEMAELGLLGMMVPPEYEGAGADAV 67 Query: 66 AYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALTE 125 +Y +AL E+A + + IMSVHNS+ C IL+ GTDEQK+R+L LA G M+GAFA+TE Sbjct: 68 SYVLALSEVAYACASTAVIMSVHNSIVCDSILHLGTDEQKQRYLPALAMGEMIGAFAMTE 127 Query: 126 PQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVP 185 P AGSD +T A +GDHY++NG K+FITSG+NAGVVIV A TDPS RGI+AF+V Sbjct: 128 PLAGSDPLRQETTAVQDGDHYIINGVKRFITSGKNAGVVIVTAKTDPSKRHRGITAFLVD 187 Query: 186 TDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGIA 245 +PG+ V R+EDK+G ASDT + FED +VP + LG EG G+ +A+ L+GGR+GIA Sbjct: 188 KGTPGFSVGRLEDKMGLRASDTADLYFEDCRVPASQILGGEGGGFSLAMKALDGGRIGIA 247 Query: 246 SQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRD 305 +QS+G+A+A +AA YA+ERE FGKPI + Q V+ LAD+AT+I AR M AA+ +D Sbjct: 248 AQSIGVAQACLDAAVKYAKEREQFGKPIGQFQGVSGPLADIATEIHAARLMALDAASRKD 307 Query: 306 SGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTSD 365 G+ +EASMAKLFASEM +V + ALQ GGYGY D+PVER YRD RV IYEGTS+ Sbjct: 308 RGQNFTMEASMAKLFASEMVNRVTAKALQIHGGYGYTKDYPVERYYRDARVFTIYEGTSE 367 Query: 366 IQRMVISRNL 375 IQR+VISR+L Sbjct: 368 IQRIVISRHL 377 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: 343 Number of extensions: 6 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: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 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