Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate AZOBR_RS31375 AZOBR_RS31375 dioxygenase
Query= SwissProt::P0CX08 (502 letters) >FitnessBrowser__azobra:AZOBR_RS31375 Length = 493 Score = 379 bits (973), Expect = e-109 Identities = 201/491 (40%), Positives = 282/491 (57%), Gaps = 9/491 (1%) Query: 12 LNAKTLKSFESTLPIPTYPREGVKQGIVHLGVGAFHRSHLAVFMHRLMQEHHLKDWSICG 71 L+ TL S P Y R + GIVHLG+GAFHR+H AV+ + W I G Sbjct: 3 LSPDTLPSLRHGAQRPGYDRAALTTGIVHLGIGAFHRAHQAVYTDDALARS-FGPWGIAG 61 Query: 72 VGLMKADALMRDAMKAQDCLYTLVERGIKDTNAYIVGSITAYMYAPDDPRAVIEKMANPD 131 V L D RDA++ Q LYT+ R ++GS+T + AP+DP AV++ + P Sbjct: 62 VSLRSPDT--RDALEPQGGLYTVAVRDAAGERLRVIGSVTQLLVAPEDPAAVLDLLTRPS 119 Query: 132 THIVSLTVTENGYYHSEATNSLMTDAPEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTP 191 IV+LTVTE GY H AT +L P+I++DL +PE P ++ G+L EAL+ R G+ P Sbjct: 120 VRIVTLTVTEKGYCHDPATGALNEAHPDIVHDLANPESPRSVPGFLVEALIRRRAAGVEP 179 Query: 192 FTIMSCDNMPQNGVTVKTMLVAFAKLKKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERK 251 FT++SCDN+P NG T +L +A+L+ D W V PNSMVDR+ P TD +R Sbjct: 180 FTVLSCDNLPSNGDTAAGLLRRYAELR-DPALGTWFAGNVACPNSMVDRIVPATTDADRD 238 Query: 252 YVADTWGIKDQCPVVAEPFIQWVLEDNFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGG 311 V+D G++D PVV EPF QWV+ED F GRP WEL G ++V DV YE MKLRLLNG Sbjct: 239 RVSDGLGLRDSWPVVTEPFSQWVIEDRFPTGRPAWELEGAELVPDVHPYETMKLRLLNGS 298 Query: 312 HSAMGYLGYLAGYTYIHEVVNDPTINKYIRVLMREEVIPLLPKVPGVDFEEYTASVLERF 371 HS + YLGYLAGY + + + DP + IR LM EE P L PG D Y +++ERF Sbjct: 299 HSTLAYLGYLAGYETVSDTMADPAFARLIRGLMDEEAGPTLHMPPGADLGHYKDALIERF 358 Query: 372 SNPAIQDTVARICLMGSGKMPKYVLPSIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNG 431 NPA++ +I + G+ K+P+ +L +I ++L LA+ VA W RY++G D G Sbjct: 359 RNPALRHRTWQIAMDGTQKLPQRLLGTIRDRL-AAGAPIDRLALGVAAWMRYVSGTDEAG 417 Query: 432 KPFEIEDPMAPTLKAAAVKGGKDPHE----LLNIEVLFSPEIRDNKEFVAQLTHSLETVY 487 +P ++ DPMA L A + G D L + +F ++ + F A +T +L +Y Sbjct: 418 RPIDVRDPMAARLAELAAEAGPDADRLATALFGLTAVFGDDLPRDPRFTAAVTDALRRLY 477 Query: 488 DKGPIAAIKEI 498 +G A ++ + Sbjct: 478 AEGARAVVQSV 488 Lambda K H 0.319 0.136 0.409 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: 719 Number of extensions: 28 Number of successful extensions: 4 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: 502 Length of database: 493 Length adjustment: 34 Effective length of query: 468 Effective length of database: 459 Effective search space: 214812 Effective search space used: 214812 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 (21.7 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