Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate Pf1N1B4_3308 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3308 Length = 371 Score = 243 bits (621), Expect = 4e-69 Identities = 141/340 (41%), Positives = 194/340 (57%), Gaps = 8/340 (2%) Query: 16 IGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYD 75 IG +L+ LNA++L M+ +L+ QLDAWA++PQ+ V+LRG G KAFCAGG++RSL + Sbjct: 17 IGIASLDAEKSLNALSLPMINALRDQLDAWAKEPQIVCVLLRGNGTKAFCAGGEVRSLVE 76 Query: 76 SFKS--GDT--LHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTE 131 + ++ G+ L FF EY LD +H Y KP++ G+VLGGGMGL+QGA +R+VT Sbjct: 77 ACRALPGEVPPLAAHFFAAEYRLDFNLHTYPKPLICWGHGYVLGGGMGLLQGASIRIVTP 136 Query: 132 RSRLAMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYCGLADWYLESNK 191 SRLAMPE+ IG +PDVG S FL R+PG+LG++LG++G Q+ DA+ LAD +L ++ Sbjct: 137 SSRLAMPEIGIGLYPDVGASWFLSRLPGKLGLFLGLTGAQMNGRDAIDLDLADRFLRDDQ 196 Query: 192 LGTLDEQLDQLQWHETPLKDLQGLLAKL---AVQQLPAAPLAALRPAIDHFFALPDVPSM 248 L E L QL W E L LL L A+ Q+P A R ID + DV Sbjct: 197 QHELIEGLLQLNWQEQTAMQLNSLLKALQQEAIAQMPQAQWLPRRELIDELLDVSDVRCA 256 Query: 249 VEQLRAVTVADSHEWATATADLLESRSPLAMGVTLEMLRRGRHLSLEQCFALELHLDRQW 308 + + A+ A + E SPL + E + R RHLSL Q F +E + Sbjct: 257 WKAISALRDHSDPLLGRAAKTMAEG-SPLTAHLVWEQIVRARHLSLAQVFQMEYTMSLNC 315 Query: 309 FERGDLIEGVRALLIDKDKNPRWSPPTLQALDAGHVASFF 348 + EGVRA LIDKD P W P + + V + F Sbjct: 316 CRHPEFSEGVRARLIDKDHKPHWHWPDINNVPEAAVEAHF 355 Lambda K H 0.322 0.138 0.422 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: 393 Number of extensions: 21 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: 356 Length of database: 371 Length adjustment: 29 Effective length of query: 327 Effective length of database: 342 Effective search space: 111834 Effective search space used: 111834 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: 49 (23.5 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