Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate AZOBR_RS31375 AZOBR_RS31375 dioxygenase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__azobra:AZOBR_RS31375 Length = 493 Score = 443 bits (1140), Expect = e-129 Identities = 240/476 (50%), Positives = 302/476 (63%), Gaps = 6/476 (1%) Query: 13 RPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENL 72 RP +D + L + IVHLG GAFHRAHQA+YT L + WGI V+L + R + L Sbjct: 17 RPGYDRAALTTGIVHLGIGAFHRAHQAVYTDDALARSFGPWGIAGVSLRSPDTR---DAL 73 Query: 73 KKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGY 132 + Q LYTVA + A L++IGS+ + L D +L+ + RP IV+LTVTEKGY Sbjct: 74 EPQGGLYTVAVRDAAGERLRVIGSVTQLLVAPEDPA-AVLDLLTRPSVRIVTLTVTEKGY 132 Query: 133 CADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENG 192 C D A+G L+ +P I HDL NP +P+S G++VEAL RR G++ FTV+SCDN+ NG Sbjct: 133 CHDPATGALNEAHPDIVHDLANPESPRSVPGFLVEALIRRRAAGVEPFTVLSCDNLPSNG 192 Query: 193 HVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAI 252 A + A+ RDP L W NV P +MVDRIVPA T ++D LG+ D + Sbjct: 193 DTAAGLLRRYAELRDPALGTWFAGNVACPNSMVDRIVPATTDADRDRVSDGLGLRDSWPV 252 Query: 253 ACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYE 312 EPF QWVIED F GRP W+ GA+ V DV P+E MKLR+LNGSHS LAYLGYL GYE Sbjct: 253 VTEPFSQWVIEDRFPTGRPAWELEGAELVPDVHPYETMKLRLLNGSHSTLAYLGYLAGYE 312 Query: 313 TIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAM 372 T++DT+ +PA+ + LM +E PTL MP G DL Y LIERF NP+LRHRTWQIAM Sbjct: 313 TVSDTMADPAFARLIRGLMDEEAGPTLHMPPGADLGHYKDALIERFRNPALRHRTWQIAM 372 Query: 373 DGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQK 432 DG+QKLPQRLL +R L G LALGVA WMRY G DE G IDV DPM A + Sbjct: 373 DGTQKLPQRLLGTIRDRLAAGAPIDRLALGVAAWMRYVSGTDEAGRPIDVRDPMAARLAE 432 Query: 433 INAQY-QGADRV-KALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486 + A+ ADR+ AL GL+ +F DDLP++ F AVT A ++L GAR V ++ Sbjct: 433 LAAEAGPDADRLATALFGLTAVFGDDLPRDPRFTAAVTDALRRLYAEGARAVVQSV 488 Lambda K H 0.320 0.135 0.408 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: 756 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 493 Length adjustment: 34 Effective length of query: 452 Effective length of database: 459 Effective search space: 207468 Effective search space used: 207468 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 (21.8 bits) S2: 52 (24.6 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