Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2523 Length = 699 Score = 190 bits (483), Expect = 2e-52 Identities = 128/399 (32%), Positives = 205/399 (51%), Gaps = 26/399 (6%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62 V VIG+G MG GI+ AG V + ++ E L + + IK + + G LK+ Sbjct: 300 VGVIGAGTMGGGISMNFLNAGIPVKILEMKQEALDRGVATIKKNYEAQVKKGKLKQDKYD 359 Query: 63 VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122 + T K D +IEAV E++ +K +F+ +A A P A+LA+NTS+L + + Sbjct: 360 QRMALLSTTLSYDDFKDCDLIIEAVFEEMGVKEAVFKQLDAVAKPGAILASNTSTLDVDK 419 Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182 IA+ K PQ VVGMHFF+P +M L+E+VRGK+T+ +V+ T + K + K ++V Sbjct: 420 IAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMAIGKKIKKTSVVSGVCD 479 Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242 GF NR++ + +L+++G + Q+VD A+E+ GF MG F + D G DIG+++ K Sbjct: 480 GFIGNRMIEQYSRQAGFLLDEG-CTPQQVD-KAVEKFGFAMGPFRMGDLAGNDIGWAIRK 537 Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPS------PGKFVRPTLPSTSKKLG 296 + + +KL G+ G K+G+G+Y Y + P V + K+LG Sbjct: 538 RRSVERADMKYSRTADKLCELGRFGQKTGAGWYDYQAGKRDAIPSDLVNKMIEDHRKELG 597 Query: 297 ------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLP---KGILSYAD 340 + L+ VNE +++L +GI K D + + G G P G + YA Sbjct: 598 ITPRKISDEEIVQRLVFALVNEGAHILEDGIASKSGDIDMVYLTGYGFPIHRGGPMHYAS 657 Query: 341 EIGIDVVVNTLEEMRQTSGMD--HYSPDPLLLSMVKEGK 377 E+G+ VV ++ + D + P PLL + EGK Sbjct: 658 EVGLFNVVQAMDRFARNPLDDAAFWKPAPLLAKLAAEGK 696 Score = 102 bits (253), Expect = 8e-26 Identities = 62/163 (38%), Positives = 89/163 (54%), Gaps = 15/163 (9%) Query: 442 VRVIAITGQGRVFSAGADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLAL 501 V+ I ITG G FS GAD+ EFG+ + V I+ KPV+A ++ +A+ Sbjct: 45 VKSIVITGAGGAFSGGADIKEFGT----DKSLQEPNLLSVIAAIENSAKPVVAAMHSVAM 100 Query: 502 GGGMELALSADFRVASKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVK 560 GGG+ELAL +R+A+ + PE+ LGLIPG GGTQRL R+ G L L+++G VK Sbjct: 101 GGGLELALGCHYRIAAPGCSIALPEVKLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVK 160 Query: 561 AEEAYRLGIV-------EFLAEPEELESEVRKLANAIAEKSPL 596 +E +G V + A E L +E A ++A+ PL Sbjct: 161 SE---MIGAVPGQKLFDKMAASAESLAAEALAFAQSVADARPL 200 Lambda K H 0.316 0.134 0.377 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: 933 Number of extensions: 59 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 699 Length adjustment: 39 Effective length of query: 612 Effective length of database: 660 Effective search space: 403920 Effective search space used: 403920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 54 (25.4 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