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 BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__BFirm:BPHYT_RS09560 Length = 694 Score = 176 bits (447), Expect = 2e-48 Identities = 127/399 (31%), Positives = 200/399 (50%), Gaps = 26/399 (6%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLK-EGV 60 +V VIG+G MG GIA AG V + + E L + + I+ + + G LK E + Sbjct: 295 QVAVIGAGTMGGGIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVL 354 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 Q +A I P T LK +D ++EAV E+L +K F+ + A A+LA+NTS+L + Sbjct: 355 GQRMALITP-TLSYDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDV 413 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 +IA+ K PQ VVGMHFF+P +M L+E+VRGK+T+ +V+ T +AK + K +V Sbjct: 414 DKIAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGV 473 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 GF NR++ + + +++E+G Q VD AIE+ GF MG F ++D G DIG+++ Sbjct: 474 CDGFIGNRMVEQYIRQALFMLEEGALPAQ-VD-KAIEKFGFAMGPFRMSDLAGNDIGWAI 531 Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPS------PGKFVRPTLPSTSK- 293 K ++L G+ G K+G G+Y Y + P K V + + SK Sbjct: 532 RKRRYLEHPDMHYSKIADRLCETGRFGQKTGGGWYDYKAGDRTAYPSKVVDDMIVAFSKE 591 Query: 294 -----------KLGRYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---KGILSY 338 ++ L+ VNE + +L EGI K D + + G G P G + Y Sbjct: 592 TDTERRKISDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLY 651 Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 AD +G+ V + D + P + + + + Sbjct: 652 ADTVGLYNVERAIRRYAARPNGDAWQLAPSIAELAAKNR 690 Score = 104 bits (259), Expect = 2e-26 Identities = 64/190 (33%), Positives = 104/190 (54%), Gaps = 6/190 (3%) Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466 +A I LN P N + I + ++ + ++ I +TG G+ FS GAD+TEF Sbjct: 11 VAVITLNNPP-VNGLGLSTRAGIVEGVERAQNDPAIKAIVLTGAGKAFSGGADITEFN-- 67 Query: 467 TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPE 526 TP + V ++ KPVIA I+ +A+GGG+ELAL A +R+A+ A++ PE Sbjct: 68 TPKAGQEPT--LATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIALPE 125 Query: 527 INLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRK 585 + LG++PG GGTQRL R G L ++++G V +E+ G+ + LA+ + E+ + Sbjct: 126 VKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFDELAQGDLAEAALAF 185 Query: 586 LANAIAEKSP 595 A++ P Sbjct: 186 ARKVSAKEGP 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: 956 Number of extensions: 57 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 694 Length adjustment: 39 Effective length of query: 612 Effective length of database: 655 Effective search space: 400860 Effective search space used: 400860 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