Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_047005493.1 AAW01_RS00825 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= SwissProt::O32178 (789 letters) >NCBI__GCF_001010925.1:WP_047005493.1 Length = 776 Score = 541 bits (1395), Expect = e-158 Identities = 308/797 (38%), Positives = 463/797 (58%), Gaps = 34/797 (4%) Query: 3 KHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLS 62 K I+K V+G+G MG+GIAA +AN G+PVLLLDI+P + + R+ ++ Sbjct: 4 KSIKKVCVIGAGTMGAGIAAQIANAGVPVLLLDILPKE--------------GDNRNAVA 49 Query: 63 RQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALV 122 A+ K+LK +PAP + + GN+EDD K+ E DW++E ++E L++K+ ++A + Sbjct: 50 EGAVAKMLKTQPAPFMGKRAAKLVETGNIEDDLGKVAECDWVVEAIIERLDIKQDLYAKL 109 Query: 123 DEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPD 182 +E R G+ VSSNTS I + ++ +GRSD FK FL THFFNP RY++L+EI+ +++ D Sbjct: 110 EEVRTPGTAVSSNTSTIPLAQLTDGRSDQFKQDFLITHFFNPPRYMRLIEIVAGPQSNAD 169 Query: 183 ILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPL 242 + ++ F + LGK VV A+D+P FIANR+GT+ + V G V E D I G Sbjct: 170 TVDMVSDFVDRKLGKTVVDAEDSPGFIANRVGTFWIQQAVNSAFDLGITVEEADEIGGRP 229 Query: 243 IGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGSKA 300 +G PK+ F +D++G+D H+ +++ D+ +++ R + M++ G+ G K Sbjct: 230 MGVPKTGLFGLIDLIGIDLMPHLMKSLTSTLPADDWYQKIARSEPLIEAMIKDGYTGRKG 289 Query: 301 GQGFYKKE----GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRA 356 GFY+ GK D L GE P L AKG +KALI + + Sbjct: 290 LGGFYRINRDGGGKVKEAKD---LKSGEYRAAARPGLVRGPAAKG---DLKALISAKGKV 343 Query: 357 GRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLE 416 G W + TL Y+A ++ E I +D AMK G+ W+ GPFEM DAIG E+L+ Sbjct: 344 GDYAWAVLGPTLSYAASIVPEATATIVGVDDAMKLGYNWKRGPFEMIDAIGAAHLVERLK 403 Query: 417 QLGADMPGWIKEMLDKGNETFYIKENGTVFYYDR-GEYRAVKENKKRIHLQALKETKGVI 475 + +P ++++ G+ TFY ++G Y+ GEY V + + L+ +K T + Sbjct: 404 ESDYPVPAILEQI---GDRTFYRVQDGKRQYFGTDGEYHDVVRPEGVLLLEDIKLTGEPL 460 Query: 476 AKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCV 535 KN A+L DLGD V LEF K NA+ ++++I K + +++YK LV+ N+G NF Sbjct: 461 IKNGSAALWDLGDGVVALEFTGKMNALDEQVMRLIQKAIPLVKKDYKALVVYNEGSNFSA 520 Query: 536 GANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAA 595 GANL + L + + EV+ ++ Q +KY+ PVV+APFG+ LGGG E CL + Sbjct: 521 GANLGLALFALNIAAWGEVEKSVKGGQAAYKALKYAPFPVVSAPFGLALGGGCEVCLNSD 580 Query: 596 RIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKVS 652 IQA +E Y+GLVE+GVG+IPG GG E+ + + R + PM A K+FE I+ A V+ Sbjct: 581 AIQAHAETYIGLVETGVGIIPGWGGCGEMISRWEENPRHPNGPMPAVSKSFELISTATVA 640 Query: 653 ASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAAL 712 SA EA++ L+ D I++N+D LLYDAKQ A ++ D G+ P K + ++PG TG AAL Sbjct: 641 KSAAEAKDHGFLRRDDGITMNRDRLLYDAKQRALAMVD-GYEAPEKPEYRLPGPTGAAAL 699 Query: 713 LLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAK 772 L + + G +EHD +A +LAYV+ GG V E+ +L+ E EAF+ L K Sbjct: 700 KLAVDSFRKQGLATEHDETVAHELAYVLTGGDTDMIDVVTEDQMLKFEAEAFMRLVRNPK 759 Query: 773 SQARMQHMLVKGKPLRN 789 SQAR++HML GKPLRN Sbjct: 760 SQARVEHMLETGKPLRN 776 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: 1473 Number of extensions: 84 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: 776 Length adjustment: 41 Effective length of query: 748 Effective length of database: 735 Effective search space: 549780 Effective search space used: 549780 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 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