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 WP_011840656.1 RSPH17029_RS04435 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_000015985.1:WP_011840656.1 Length = 733 Score = 189 bits (481), Expect = 3e-52 Identities = 129/396 (32%), Positives = 200/396 (50%), Gaps = 24/396 (6%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLK-EGV 60 K+ VIG+G+MG GIA +AA AG EV + D + E + + L K + G + E Sbjct: 329 KLGVIGAGMMGAGIAHVAANAGIEVVLIDATQEAADRGKAHSEGLLDKGMKRGKVSAEKK 388 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 +VL RI TD A AL G D ++EAV ED +K + + EA P + ATNTS+LPI Sbjct: 389 AEVLGRIAATTDYA-ALSGCDLIVEAVFEDPAVKAEVTQKVEAAVGPDCIFATNTSTLPI 447 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 S +A + P + +G+HFF+P M LVEI+RGK T D V + + + K IVV D Sbjct: 448 SGLAKASRDPAQFIGIHFFSPVDKMMLVEIIRGKATGDRAVAKALDFVRQIRKTPIVVHD 507 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 F+ NR ++ + G +V +G+A + +A + +G P+G L D T +D+G + Sbjct: 508 ARFFYANRCIIPYLNEGIRMVAEGVA--PALIENAAKLVGMPLGPLQLVDETSIDLGVKI 565 Query: 241 WKAVTARGFKAFPCSSTE----KLVSQGKLGVKSGSGYYQYPSPGKF------------V 284 KA A +A+P ++ + L +G+LG K+G+G+Y Y + GK + Sbjct: 566 AKATKAALGEAYPDAAVDAVIFPLADEGRLGRKAGAGFYAYDAAGKRDGLWPGLADRWPL 625 Query: 285 RPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILSYADE 341 T P ++ R L + + V L + + + G +LG G G S+ D Sbjct: 626 AETQPELAEVQHRLLFAQVLEAVRALEEGVLTDIREGDVGAILGWGFAPWSGGPFSWLDM 685 Query: 342 IGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 IG V E + + G ++P LL+ M +G+ Sbjct: 686 IGAPRAVEICEGLAERHG-TRFAPPKLLVEMAGKGE 720 Score = 64.3 bits (155), Expect = 2e-14 Identities = 49/177 (27%), Positives = 88/177 (49%), Gaps = 19/177 (10%) Query: 428 EINQALDSLEEREDVRVIAITGQGRVFSAGADVT------EFGSLTPVKAMIAS-RKFHE 480 E++ + + + V+ + +T + F+AG D+ E G P +A+ + H Sbjct: 35 ELDGLIAAALDDPSVKGVILTSGKKDFAAGMDLNVIARMKEEGGDDPARAVFEGVMEMHA 94 Query: 481 VFMKIQFLT---------KPVIAVINGLALGGGMELALSADFRVASKT--AEMGQPEINL 529 V +I+ KP++A + G ALG G+EL L+ +A+ A++G PEI + Sbjct: 95 VLRRIERAGMDPKTLKGGKPIVAALPGTALGLGLELPLACHRIIAADNPKAKIGLPEIMV 154 Query: 530 GLIPGGGGTQRL-SRLSGRKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRK 585 G+ PGGGGT RL RL L+L G+ + A +G+V+ + ++L + ++ Sbjct: 155 GIFPGGGGTTRLVRRLGAMMAAPLLLEGKLNDPKGAKAMGVVDEVVPADQLLARAKE 211 Score = 42.4 bits (98), Expect = 8e-08 Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 8/94 (8%) Query: 300 ISPAVNEVSYLLREGIVGK--DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQT 357 I P +NE ++ EG+ ++A K +G+P G L DE ID+ V + + Sbjct: 517 IIPYLNEGIRMVAEGVAPALIENAAKL----VGMPLGPLQLVDETSIDLGVKIAKATKAA 572 Query: 358 SGMDH--YSPDPLLLSMVKEGKLGRKSGQGFHTY 389 G + + D ++ + EG+LGRK+G GF+ Y Sbjct: 573 LGEAYPDAAVDAVIFPLADEGRLGRKAGAGFYAY 606 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: 1016 Number of extensions: 63 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: 3 Length of query: 651 Length of database: 733 Length adjustment: 39 Effective length of query: 612 Effective length of database: 694 Effective search space: 424728 Effective search space used: 424728 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 Apr 10 2024. 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