Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate CA265_RS17590 CA265_RS17590 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::O32178 (789 letters) >FitnessBrowser__Pedo557:CA265_RS17590 Length = 802 Score = 731 bits (1888), Expect = 0.0 Identities = 392/802 (48%), Positives = 521/802 (64%), Gaps = 14/802 (1%) Query: 1 MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60 M + I K AVLGSG+MGS IA H ANIG+ VLLLDI P +L+ EE+ KGLT D+ V++R Sbjct: 2 MKRSINKVAVLGSGIMGSRIACHFANIGVEVLLLDIAPKELSPEEQAKGLTLDNPAVKNR 61 Query: 61 LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120 + A++ +K P+P+ + K + I GN DD K+ DW+IEVVVENL++KKK+F Sbjct: 62 IVNTALQTAVKTNPSPVYTKKALNKIKTGNFADDMSKIAGYDWVIEVVVENLDIKKKVFE 121 Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180 V++ RK G++++SNTSGI + MAEGRS+DFKAHF GTHFFNP RYLKLLEIIP T Sbjct: 122 QVEQFRKPGTLITSNTSGIPIHLMAEGRSEDFKAHFCGTHFFNPPRYLKLLEIIPTPHTQ 181 Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240 P+I+ F+ +G+ LGK V KDTP FIANR+G Y ++ + + K V EVD TG Sbjct: 182 PEIVDFLMHYGDKFLGKTTVLCKDTPAFIANRVGVYSIMALLHLVEKLDLTVEEVDKFTG 241 Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299 P +GRPKSATFRT DVVGLDT VA+ +YD D+ ++F++P+++ M E W+G K Sbjct: 242 PALGRPKSATFRTSDVVGLDTMIKVAKGLYDNCPDDKAHDLFKLPAYVQKMEENKWLGDK 301 Query: 300 AGQGFYKK----EGKT-IYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354 QGFYKK +GKT I LD TL Y + K+KS LE K + + +MK D Sbjct: 302 TQQGFYKKTKSADGKTEILALDLKTLEYKPQQKVKSATLEMTKPIENLRERMKIFAKGKD 361 Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414 +AG L + + Y ++ + EI+D+++ ID AM+ GFGWELGPFE+WDA+G+K++ E Sbjct: 362 KAGELFRHSSFGLFEYVSDRIPEISDELYRIDDAMRAGFGWELGPFELWDAVGVKEAIEG 421 Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472 +EQ G W+ EMLD GN +FY ENG YYD Y+A+ + I L L+E K Sbjct: 422 MEQYGNKAAAWVHEMLDAGNTSFYKVENGVKKYYDIPSKSYKALPGTDEFIILDNLRENK 481 Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532 + KNSG S+IDLGD + +EFH+K N IG D+I I+K ++ E++Y+GLVIGN G N Sbjct: 482 -TLWKNSGVSIIDLGDGILNVEFHTKMNTIGGDVISGINKAIDMAEKDYRGLVIGNDGAN 540 Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592 F GAN+ MI M + + E++ IR FQ T M+I+YS+ PVV AP +TLGGG E L Sbjct: 541 FSAGANVGMIFMMAVEQEWDELNMAIRMFQNTSMRIRYSSIPVVVAPHNLTLGGGCEFSL 600 Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKELYINHLRRGHDP---MNAAMKTFETIAMA 649 A +Q ++E YMGLVE GVG+IPGGGG KE + D NA F TI MA Sbjct: 601 HADHVQLSAETYMGLVEFGVGVIPGGGGTKEFALRASDEYKDDQIVQNALKDRFLTIGMA 660 Query: 650 KVSASAQEAREMNIL-KETDQISVNQDHLLYDAKQLAASLYDTGWRPPV-KEKVKVPGET 707 KVS S EA E+ L K+ IS+N++ LL DAK A L D G+ PV + +KV G+ Sbjct: 661 KVSTSGYEAYELGYLQKDKFSISMNRNRLLADAKAKAIELADAGYTKPVQRNDIKVLGKQ 720 Query: 708 GYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSL 767 G + GA M +ISEHD KI++KL YV+ GG + TEV E+YLL++EREAFLSL Sbjct: 721 GLGIVYAGANSMYAGHFISEHDKKISEKLGYVMCGGDLSAPTEVTEQYLLDLEREAFLSL 780 Query: 768 SGEAKSQARMQHMLVKGKPLRN 789 +GE KS R+Q ++ KGKPLRN Sbjct: 781 AGERKSLERIQSIITKGKPLRN 802 Lambda K H 0.316 0.134 0.382 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: 1492 Number of extensions: 76 Number of successful extensions: 6 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: 789 Length of database: 802 Length adjustment: 41 Effective length of query: 748 Effective length of database: 761 Effective search space: 569228 Effective search space used: 569228 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: 55 (25.8 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