Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_009547881.1 CCE_RS14550 AMP-dependent ligase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000017845.1:WP_009547881.1 Length = 1261 Score = 171 bits (433), Expect = 1e-46 Identities = 114/355 (32%), Positives = 182/355 (51%), Gaps = 5/355 (1%) Query: 14 VRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYVAYAMALEE 73 +R +A E + + D+ P + + GL GM VP ++GG + +E+ Sbjct: 597 LRNYANEHIN--SRLMDERRCIPPHIVLDFGNQGLLGMQVPPEYGGLGLNHGETMKVIEQ 654 Query: 74 IAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTEPQAGSDAS 133 + A D S + ++N +G P+L+FG++ KE+ L LATG L AFALTEP AGS+ Sbjct: 655 LGAIDTTLSLFVGLNNILGIRPLLQFGSQALKEELLPMLATGRELAAFALTEPSAGSNPQ 714 Query: 134 SLKTRAR-LEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGK-RGISAFIVPTDSPGY 191 ++ + A L D +VLNG+K + S AGV+ VF GK +GIS+F V +PG Sbjct: 715 AITSSAMPLSSDKWVLNGTKIWSGSAAWAGVINVFVQQKDAQGKFQGISSFAVRRGTPGL 774 Query: 192 QVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIGIASQAVGM 251 + LG + +NV V + +LG GEG K+A + GR+ IA+ +VG Sbjct: 775 KQGPEALTLGMRGMVQNTVYLNNVPVSASQQLGDPGEGMKVAQDAMMYGRLAIAAASVGG 834 Query: 252 ARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAALRDAGRPAL 311 + ++ Y++ RQ L+++ V RL + I+ +V A L D G+ Sbjct: 835 MKRCAQLWHRYSSRRQISTGRLLDNPLVLARLNGLTAAITTVETLVTSIAQLLDQGQEVP 894 Query: 312 VEA-SMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSD 365 +EA ++ K+ A E + + +Q LGG GY+ +I RD RV +I+EG ++ Sbjct: 895 IEAYTVCKMAAPEFYWQAADNLVQFLGGRGYIETNIAPQILRDARVLRIFEGPTE 949 Lambda K H 0.319 0.134 0.382 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: 878 Number of extensions: 43 Number of successful extensions: 4 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: 1261 Length adjustment: 39 Effective length of query: 336 Effective length of database: 1222 Effective search space: 410592 Effective search space used: 410592 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: 54 (25.4 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