Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate AZOBR_RS20225 AZOBR_RS20225 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::O32178 (789 letters) >FitnessBrowser__azobra:AZOBR_RS20225 Length = 777 Score = 507 bits (1306), Expect = e-148 Identities = 310/798 (38%), Positives = 442/798 (55%), Gaps = 36/798 (4%) Query: 5 IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64 I++AAV+GSGVMGSGIAAH AN GIPV+LLDI + + RS +++ Sbjct: 3 IKRAAVIGSGVMGSGIAAHFANAGIPVVLLDIPAKE--------------GDDRSAIAKG 48 Query: 65 AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124 A+++LLK PAP KN +TPGNLEDD L + DWI+E +VEN VK ++ +D Sbjct: 49 AVQRLLKTDPAPFMHPKNAKLVTPGNLEDDLALLADVDWIVEAIVENPAVKADLYRRIDP 108 Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184 RK GS+VSSNTS I + + EG+SD F+ FL THFFNP RY++LLEI+ + T PD L Sbjct: 109 VRKAGSVVSSNTSTIPLGVLVEGQSDAFRRDFLITHFFNPPRYMRLLEIVGGEATRPDAL 168 Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244 + + LGKGVV KDTP FIANRIG Y + + + G V E D+I G +G Sbjct: 169 AAVADVCDRALGKGVVRCKDTPGFIANRIGVYWIQTAINAAVDLGLTVEEADAIVGRPMG 228 Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGSKAGQ 302 PK+ F +D+VGLD H+A+++ ++ + FR + M+ +G+ G K Sbjct: 229 IPKTGVFGLVDLVGLDLMPHIAKSLLATLPENDPYRAAFREHPVITRMIAEGYTGRKGKG 288 Query: 303 GFYKKE---GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRL 359 GFY+ G + E+ + L+ G + P LE+ ++AL D+ G+ Sbjct: 289 GFYRLNRDGGAKVKEV--IDLSTGAYRRSDKPKLESVST---VGRDLRALADFPDKTGQY 343 Query: 360 LWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLG 419 + + TL Y+A L+ EIAD I A+D+ M+ G+ W+ GPFE+ D +G A+ G Sbjct: 344 ARRVLAHTLAYAASLVPEIADSIVAVDEGMRLGYNWKQGPFELIDRLGTAWFADLCRSEG 403 Query: 420 ADMPGWIKEMLDKGNETFYIKENGTVFYY-DRGEYRAVKENKKRIHLQALKETKGVIAKN 478 +P +++ FY E+G + + G Y V + L +K + KN Sbjct: 404 IPVPALVEQ---AAGRPFYRVEDGRLQHLTTAGLYDTVVRPDGVLLLSDIKRASQPVWKN 460 Query: 479 SGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLE---ETERNYKGLVIGNQGKNFCV 535 ASL D+GD V +EF SK NA+ D++ K ++ + + N+K LVI N+ NF V Sbjct: 461 GSASLWDIGDGVLCVEFTSKMNALDGDVMAAYGKAMKLIGDGKGNWKALVIHNESDNFSV 520 Query: 536 GANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAA 595 GANL + L + + +++ ++ Q +KY+ PVV+AP GM LGGG E L + Sbjct: 521 GANLGLALFALNVGLWPQIEELVEGGQRAYRALKYAPFPVVSAPSGMALGGGCEILLHSD 580 Query: 596 RIQAASEAYMGLVESGVGLIPGGGGNKELYINHL---RRGHDPMNAAMKTFETIAMAKVS 652 +QA +E YMGLVE GVGLIPG GG E+ H R PM FETI++AKV+ Sbjct: 581 HVQAHAETYMGLVEVGVGLIPGWGGCTEMLARHAANPRTPKGPMPPIAGAFETISLAKVA 640 Query: 653 ASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAAL 712 SA EA+++ L+ +D I++N+D LL DAK A L + PP K +PG G AAL Sbjct: 641 KSAAEAKDLLYLRASDGITMNRDRLLADAKAKALEL-AANYTPPEKVTYTLPGPNGRAAL 699 Query: 713 LLGAEQMKLSGYISEHDFKIAKKLAYVIAGG-KVPFGTEVDEEYLLEIEREAFLSLSGEA 771 L E L G + HD + KLA ++ GG K V E+ +L +ER AF+ L Sbjct: 700 ELFLEGFALQGKATPHDMVVCGKLAGILTGGPKADVTQPVTEDQMLALERRAFMELVRTE 759 Query: 772 KSQARMQHMLVKGKPLRN 789 + R++HML GKPLRN Sbjct: 760 GTIDRVEHMLTTGKPLRN 777 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: 1348 Number of extensions: 70 Number of successful extensions: 9 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: 777 Length adjustment: 41 Effective length of query: 748 Effective length of database: 736 Effective search space: 550528 Effective search space used: 550528 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 Apr 09 2024. 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