Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_057507561.1 ABB28_RS04905 enoyl-CoA hydratase/isomerase family protein
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >NCBI__GCF_001431535.1:WP_057507561.1 Length = 393 Score = 230 bits (587), Expect = 5e-65 Identities = 150/377 (39%), Positives = 195/377 (51%), Gaps = 47/377 (12%) Query: 31 IGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAGGDIRALYD 90 IG+ TLN PR LN S PM LL +L AWA IA VVL+GAG KAFCAGGD+ +LY Sbjct: 27 IGVATLNAPRTLNGFSLPMAHLLLERLQAWADDGQIAMVVLQGAGEKAFCAGGDLHSLYQ 86 Query: 91 SF-------HAGT---ALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQAAH 140 S HA A +FF EY++D+ +H YPKP++ GIVMGGG+GL A Sbjct: 87 SMLAYRAAGHADVRTNAYAAEFFDVEYRVDFLIHTYPKPILCWGHGIVMGGGIGLMSGAS 146 Query: 141 LRVLTERSRVAMPETGIGLVPDVGASHFLSKLPLALALYVGLTGVTLGAADTLLCKLADI 200 RV++ERS++A PE +GL PDVG S L ++P L++ LTG LG D + LAD+ Sbjct: 147 HRVVSERSKLAFPEITVGLFPDVGGSWLLQRVPGKAGLFLALTGALLGPGDAIHADLADL 206 Query: 201 AVPAAS-LEHFEQTLAAINRTGDVLADLRAALQATPDAGEQAAPLQSVLPAVLRHFRADA 259 + A E F+ A LQA + +A L +L+ F +DA Sbjct: 207 HIAEAQRAEVFD-----------------ALLQADWSSDNEAN--HGRLDTLLQSFASDA 247 Query: 260 ------SVAGLLDSLAAESD-PAYAD----------WAARTLDILRGRSPLMMAVTRELL 302 S AGLLD+L A + PA + W L +P + EL Sbjct: 248 PAGPLQSHAGLLDTLCAGDELPAIIERIGALQTEDAWLQNAQKTLVAGAPGSARLAFELQ 307 Query: 303 LRGRDLDLADCFRMELGVVSHAFSQGDFIEGVRALIVDKDNAPRWRVKDASEVSEAVVQS 362 R DLA +R+E H + GDF EG+RAL+VDKD P W ++ S A + Sbjct: 308 RRAAGADLATVYRLEYVTALHCAAHGDFAEGIRALLVDKDRTPHWNPATLADASAAWAED 367 Query: 363 FFDSPWPREPHPLAMLG 379 FF SPWP + HPLA LG Sbjct: 368 FFISPWPADQHPLADLG 384 Lambda K H 0.322 0.137 0.405 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: 389 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 393 Length adjustment: 30 Effective length of query: 354 Effective length of database: 363 Effective search space: 128502 Effective search space used: 128502 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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