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 RR42_RS11095 RR42_RS11095 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Cup4G11:RR42_RS11095 Length = 693 Score = 184 bits (468), Expect = 9e-51 Identities = 129/399 (32%), Positives = 203/399 (50%), Gaps = 26/399 (6%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSL-KEGV 60 +V VIG+G MG GI AG V M + E L + + I+ + + G L +E V Sbjct: 294 RVAVIGAGTMGGGITMNFLNAGVPVIMLETKQEALDRGVATIRKNYENSAKKGKLTQEKV 353 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 EQ + + T +K +D VIEAV E++ +K +F+ + A+LA+NTS+L + Sbjct: 354 EQRMGLL-TTTLSYDEIKDADMVIEAVFEEMGVKEIVFKKLDEVMKQGAILASNTSTLDV 412 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 ++IAS K PQ VVGMHFF+P +M L+E+VRG+ T +V+ T ++AK + K +V Sbjct: 413 NKIASFTKRPQDVVGMHFFSPANVMKLLEVVRGEKTGKDVLATVMQLAKKIKKTAVVSGV 472 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 GF NR++ + YL+++G ++ E AIE+ GF MG F + D G DIG+++ Sbjct: 473 CDGFIGNRMIEQYSRQAGYLLDEG--ALPEQVDKAIEKFGFAMGPFRMGDLAGNDIGWAI 530 Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY------PSPGKFVRPTLPSTSKK 294 K + + + L G+ G K+G+G+Y Y P P + V + SK Sbjct: 531 RKRRAIDKPEIQYSKTADLLCELGRYGQKTGAGWYDYKAGDRKPYPNQQVNDMIVQHSKD 590 Query: 295 LG------------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---KGILSY 338 LG L+ VNE + +L EGI K D + + G G P G + Y Sbjct: 591 LGITRRKISDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLFRGGPMLY 650 Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 AD++G+ V ++ + + + PLL+ + EGK Sbjct: 651 ADQVGLFNVAQSMARYAKGYHGEAWQAAPLLVKLAAEGK 689 Score = 108 bits (269), Expect = 1e-27 Identities = 70/206 (33%), Positives = 111/206 (53%), Gaps = 20/206 (9%) Query: 398 TIVVRVEPPLAWIVLNRPTRYNAING-------DMIREINQALDSLEEREDVRVIAITGQ 450 T +V+ +A I L+ P +NG ++ + +ALD V+ I ITG Sbjct: 2 TAQYQVQDGVAVITLDNPP----VNGLGLSTRLGIVEGMTRALDDAA----VKAIVITGA 53 Query: 451 GRVFSAGADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALS 510 G+ FS GAD+ EF TP + H V ++ +KPV+A I+ +A+GGG+ELAL Sbjct: 54 GKAFSGGADIREFN--TPKATQEPT--LHSVIKVVEGSSKPVVAAIHSVAMGGGLELALG 109 Query: 511 ADFRVASKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGI 569 ++RVASK A++ PE+ LGL+PG GGTQRL R+ G L ++++G + +E+ + Sbjct: 110 CNYRVASKGAQIALPEVKLGLLPGAGGTQRLPRVIGLEAALNMIVSGNAIPSEKFAGTKL 169 Query: 570 VEFLAEPEELESEVRKLANAIAEKSP 595 + + + + L + V A A P Sbjct: 170 FDEIVDGDVLPAAVAFAKTAAANPGP 195 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: 979 Number of extensions: 52 Number of successful extensions: 9 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: 693 Length adjustment: 39 Effective length of query: 612 Effective length of database: 654 Effective search space: 400248 Effective search space used: 400248 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