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_022950068.1 H035_RS0116520 crotonase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_000421465.1:WP_022950068.1 Length = 677 Score = 187 bits (475), Expect = 1e-51 Identities = 135/371 (36%), Positives = 195/371 (52%), Gaps = 14/371 (3%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62 V V+G+G MG IA G + D + A++R + L K R +E + Sbjct: 306 VHVVGAGTMGGDIAAWCVSRGLTAGLQDREPRYIAPAVKRA-YRLFKRRFKAKHEETAAR 364 Query: 63 VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122 R+ P++ Q + +D VIEA+ E+L KR ++R E+ +P A+LATNTSSLP+ E Sbjct: 365 --DRLIPDSKGFQVDR-ADIVIEAIVENLNAKRALYREIESKLAPDALLATNTSSLPLEE 421 Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182 +A L+ P+R+VGMHFFNP M LVE+VRG T + V A +++++ + VK P Sbjct: 422 LAEGLQHPERLVGMHFFNPVAKMQLVEVVRGSHTDEGVADRAAAFVRAIDRLPLPVKSAP 481 Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242 GF VNRVL+ + L+E+GI + VD +A E G PMG LAD GLDI +V + Sbjct: 482 GFLVNRVLMPYLLEAVVLLEEGIPA-DAVDRAA-TEFGMPMGPIRLADTVGLDICLAVAE 539 Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYP--SPGKFVRPTLPSTSKKLGRYLI 300 +T P +K V+ G+LGVKSG+G+Y+Y P + + P + + LI Sbjct: 540 ILTENLGGEVPRLLRDK-VAAGELGVKSGTGFYRYKRGKPIVWRKSASPLPQETIEERLI 598 Query: 301 SPAVNEVSYLLREGIVGKDD-AEKGCVLGLGLPK---GILSYADEIGIDVVVNTLEEMRQ 356 +NE +LRE +V D + G V G G G + Y + GI LEE Sbjct: 599 LRLLNECVAVLREQVVEDADLVDAGMVFGAGFAPFRGGPMHYLRQRGIAETQQKLEEFAS 658 Query: 357 TSGMDHYSPDP 367 T G + PDP Sbjct: 659 TYG-PRFQPDP 668 Score = 93.2 bits (230), Expect = 3e-23 Identities = 63/176 (35%), Positives = 99/176 (56%), Gaps = 6/176 (3%) Query: 407 LAWIVLNRP-TRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGS 465 +AW+ + + N ++ D++ E+ LD + ++ ++ + F AGADV EF Sbjct: 16 IAWLHFDHAESNANVLSADVLAELGSVLDRFHKNPPRGLVILSDKPSGFIAGADVKEFIQ 75 Query: 466 LTPV-KAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAE--M 522 LT +A+ + H+ + L P +A I+G LGGG+ELAL+ +RVA A+ + Sbjct: 76 LTERHRALSLIQVAHKRLQSLATLPCPTVARIHGYCLGGGLELALACRYRVALDDAKTRL 135 Query: 523 GQPEINLGLIPGGGGTQRLSRLSGRKG-LELVLTGRRVKAEEAYRLGIVEFLAEPE 577 G PE+ LG+ PG GG+ RL R G +L+L+GR V A +A RLG+V+ A PE Sbjct: 136 GLPEVLLGIHPGFGGSVRLIRRIGAPAAFQLMLSGRTVDAAKAARLGLVDH-AVPE 190 Score = 48.5 bits (114), Expect = 1e-09 Identities = 45/160 (28%), Positives = 67/160 (41%), Gaps = 19/160 (11%) Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358 ++ P + E LL EGI DA G+P G + AD +G+D+ + E + + Sbjct: 488 VLMPYLLEAVVLLEEGIPA--DAVDRAATEFGMPMGPIRLADTVGLDICLAVAEILTENL 545 Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTIVVRVEPPLAWIVLNRPTRY 418 G + LL V G+LG KSG GF+ Y + P+ W P Sbjct: 546 GGE---VPRLLRDKVAAGELGVKSGTGFYRYKRGK------------PIVWRKSASPLPQ 590 Query: 419 NAINGDMI-REINQALDSLEEREDVRVIAITGQGRVFSAG 457 I +I R +N+ + L E + V + G VF AG Sbjct: 591 ETIEERLILRLLNECVAVLRE-QVVEDADLVDAGMVFGAG 629 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: 878 Number of extensions: 41 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: 677 Length adjustment: 38 Effective length of query: 613 Effective length of database: 639 Effective search space: 391707 Effective search space used: 391707 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 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