Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate Echvi_1069 Echvi_1069 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::O32178 (789 letters) >FitnessBrowser__Cola:Echvi_1069 Length = 801 Score = 709 bits (1830), Expect = 0.0 Identities = 382/803 (47%), Positives = 521/803 (64%), Gaps = 16/803 (1%) Query: 1 MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60 M + I+K A+LGSGVMGS IA H ANIG+ VLLLDI+P + + E KKGL+ + VR+R Sbjct: 1 MKRAIQKVAILGSGVMGSRIACHFANIGVKVLLLDILPKEPNEAESKKGLSLEDKAVRNR 60 Query: 61 LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120 L +A++K LK KP+P+ I GN +DD K+K+ DW+IEVVVE L++K+ ++ Sbjct: 61 LVNEALEKTLKSKPSPIYDRAFADRIQTGNFDDDLPKIKDYDWVIEVVVERLDIKQSLYE 120 Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180 V++HRK G++++SNTSGI +Q + EGRSDDF+A+F GTHFFNP RYL+LLEIIP +TD Sbjct: 121 KVEQHRKPGTLITSNTSGIPMQMLCEGRSDDFQANFCGTHFFNPPRYLRLLEIIPGPKTD 180 Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQ--EMLKGGYQVGEVDSI 238 P I+ F+ +G+ LGK V KDTP FIANRIG Y ++ ++ E +K G V EVD + Sbjct: 181 PAIIDFLMDYGDRHLGKETVLCKDTPAFIANRIGVYAMMSSMHIIESMKMG--VSEVDKL 238 Query: 239 TGPLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIG 297 TG +IGR KSATFRT+DVVGLDT +VA N+ DE K+ F++P + + EK W+G Sbjct: 239 TGTVIGRAKSATFRTMDVVGLDTMVNVANNLSKALQNDESKDKFKLPKTVAYLSEKKWLG 298 Query: 298 SKAGQGFY-----KKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYS 352 K GQGF+ K K + E+D T Y K K ALEA+K+ K ++K L+ Sbjct: 299 DKTGQGFFHMIRHKDGSKELKEIDLQTHEYKPAEKPKFKALEASKEINDLKERIKFLVNF 358 Query: 353 DDRAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSA 412 DD AG Y + + EI+D+++ IDQA+ GFGWE GPFE WD +GLK + Sbjct: 359 DDEAGAFYRATFYDLFRYCSFRIPEISDELYRIDQAVCAGFGWEYGPFENWDILGLKDTI 418 Query: 413 EKLEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKE 470 +K+E+ WI EMLD GNE FY E+G YYD Y+ + ++ I L LK Sbjct: 419 KKMEEADQRPAEWIYEMLDAGNEHFYRVEDGRRQYYDIPSKSYKDIPGQQEFILLDTLKA 478 Query: 471 TKGVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQG 530 I N+GA++ D+GD+V LEFH+K N++G ++I+ I+ + E++YKGLVIGN+G Sbjct: 479 ANKKIWGNAGATIYDMGDEVIGLEFHTKMNSLGQEVIEGINTAITMAEKDYKGLVIGNEG 538 Query: 531 KNFCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEA 590 NF GANLAM+ M D F E++ +I +FQ+TMM+++YS+ PVV AP M LGGG E Sbjct: 539 ANFSAGANLAMLFMFAGDQEFDEINLMIAQFQKTMMRVRYSSVPVVVAPHNMALGGGCEM 598 Query: 591 CLPAARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIA 647 L A +QA +E YMGLVE GVGLIP GGG KE+ + N + G +N + F IA Sbjct: 599 SLHADAVQAHAELYMGLVEFGVGLIPAGGGTKEMILRFSNAIHSGDVEVNRLQEYFMNIA 658 Query: 648 MAKVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKE-KVKVPGE 706 AKVS SA+EAR + L+ D I++N+ +AK L+D G+ PV++ +KV G+ Sbjct: 659 TAKVSTSAEEARGLGYLQAKDDITLNRKRQFAEAKAKVIELFDEGYTQPVQQTNIKVLGK 718 Query: 707 TGYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLS 766 T A G M+ YISEHD KIA+KLA+V++GG + EV E+YLLE+EREAFLS Sbjct: 719 TSLALFEAGITGMRYGAYISEHDAKIARKLAWVMSGGDLSQANEVSEQYLLELEREAFLS 778 Query: 767 LSGEAKSQARMQHMLVKGKPLRN 789 L+GE K+ R+Q +L KGKPLRN Sbjct: 779 LTGEQKTLERIQSILFKGKPLRN 801 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: 1505 Number of extensions: 73 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: 801 Length adjustment: 41 Effective length of query: 748 Effective length of database: 760 Effective search space: 568480 Effective search space used: 568480 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