Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AZOBR_RS31375 AZOBR_RS31375 dioxygenase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__azobra:AZOBR_RS31375 Length = 493 Score = 296 bits (757), Expect = 1e-84 Identities = 165/428 (38%), Positives = 239/428 (55%), Gaps = 6/428 (1%) Query: 2 ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHA-PDWAIVGV 60 ++ +TL SL Q P YD + GIVH G+G F RAH+A Y + L + W I GV Sbjct: 3 LSPDTLPSLRHGAQRPGYDRAALTTGIVHLGIGAFHRAHQAVYTDDALARSFGPWGIAGV 62 Query: 61 GLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVD 120 L RS + + Q LY++ +G+ +RV+G++ L+AP DP AVL L Sbjct: 63 SL----RSPDTRDALEPQGGLYTVAVRDAAGER-LRVIGSVTQLLVAPEDPAAVLDLLTR 117 Query: 121 PAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGG 180 P++RIV++T+TE GY + TGA + + + DL NPE P +V G++VEAL RR AG Sbjct: 118 PSVRIVTLTVTEKGYCHDPATGALNEAHPDIVHDLANPESPRSVPGFLVEALIRRRAAGV 177 Query: 181 KAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIA 240 + FTV+SCDNL NG+ A YA+ RDP L W N PN MVDRI P + Sbjct: 178 EPFTVLSCDNLPSNGDTAAGLLRRYAELRDPALGTWFAGNVACPNSMVDRIVPATTDADR 237 Query: 241 KKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNA 300 +++ GL D P+V E F QWV+ED+F GRP E G ++V DV +E +K+R+LN Sbjct: 238 DRVSDGLGLRDSWPVVTEPFSQWVIEDRFPTGRPAWELEGAELVPDVHPYETMKLRLLNG 297 Query: 301 GHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISR 360 H L + G L GYE V D + D ++ ++++ PTL P G L Y+D++I R Sbjct: 298 SHSTLAYLGYLAGYETVSDTMADPAFARLIRGLMDEEAGPTLHMPPGADLGHYKDALIER 357 Query: 361 FSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKG 420 F N A+ +T +IA DG K+ T+R + + R+A G+A+++ + G DE G Sbjct: 358 FRNPALRHRTWQIAMDGTQKLPQRLLGTIRDRLAAGAPIDRLALGVAAWMRYVSGTDEAG 417 Query: 421 GTYESSEP 428 + +P Sbjct: 418 RPIDVRDP 425 Lambda K H 0.317 0.135 0.398 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: 626 Number of extensions: 25 Number of successful extensions: 2 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: 485 Length of database: 493 Length adjustment: 34 Effective length of query: 451 Effective length of database: 459 Effective search space: 207009 Effective search space used: 207009 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: 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