Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate AZOBR_RS04835 AZOBR_RS04835 methanol dehydrogenase
Query= BRENDA::P18278 (742 letters) >FitnessBrowser__azobra:AZOBR_RS04835 Length = 559 Score = 304 bits (778), Expect = 9e-87 Identities = 195/543 (35%), Positives = 282/543 (51%), Gaps = 53/543 (9%) Query: 60 RTYSEQRYSPLDQINRSNVGDLKLLGYYTLDTNRGQEATPLVVDGIMYATTNW-SKMEAL 118 + Y+ RYS LD+I+ + V DL++ ++ RG EA PLVV+ MY T + +K+ AL Sbjct: 4 KNYTSTRYSELDEIDTNTVRDLQVSFTFSTGVVRGHEAAPLVVNDTMYVVTPYPNKLYAL 63 Query: 119 DAAT--GKLLWQYDPKVPGNIADKGCCDTVNRGAGYWNGKVFWGTFDGRLVAADAKTGKK 176 D W ++P+ + CCD VNRG + +G++F T D + VA DA+TG++ Sbjct: 64 DLTKPGAPAKWTFEPRPAASAQGVACCDYVNRGPAFADGRIFINTLDAQTVAVDAETGRE 123 Query: 177 VWAVNTIPADASLGKQRSYTVDGAVRVAKGLVLIGNGGAEFGARGFVSAFDAETGKLKWR 236 VW T D + G+ T+ A V KG VL+GN G EFG RG+++A DA TGK+ WR Sbjct: 124 VW--RTKLGDINKGE----TMTMAPLVVKGKVLVGNAGGEFGVRGWITALDAGTGKIVWR 177 Query: 237 FYTVPNNKNEPDHAASDNILMNKAYK--------------TWGPKGAWVRQGGGGTVWDS 282 Y PD ++L+ YK TW P AW + GGGTVW Sbjct: 178 AYNTG-----PDQ----DVLIGDDYKPFYDKEKGKDLGVGTW-PPNAW--EIGGGTVWGW 225 Query: 283 LVYDPVSDLIYLAVGNGSPWNYKYRSEGIGSNLFLGSIVALKPETGEYVWHFQATPMDQW 342 + YDP DLIY GN PWN + R G N + G I A P+TG+ W +QA P D + Sbjct: 226 ISYDPELDLIYHGTGNPGPWNPEQRP---GDNKWTGGIFARNPDTGQARWFYQAVPHDLY 282 Query: 343 DYTSVQQIMTLDMPVKGEMRHVIVHAPKNGFFYVLDAKTGEFLSGKNYVYQNWANGLDPL 402 DY + +++ LD+P +G+ R V++ +NG+ YV+D +GE L+ Y N G+D Sbjct: 283 DYDGINELILLDLPWQGQPRKVLIRPERNGYLYVIDRSSGEVLAADPYFPANSTKGVDLK 342 Query: 403 TGRPMYNPDGLYTLNGKFWYGI-PGPLGAHNFMAMAYSPKTHLVYIPAHQIPFGYKNQVG 461 TG YN + + GK I P GA ++ A+SPKT VYIP + + +++ Sbjct: 343 TGLIEYNEE-KHPRVGKVVRDICPTAPGAKDWNPSAFSPKTGNVYIPHNNLCMDWESVEA 401 Query: 462 GFKPHADSWNVGLDMTKNGLPDTPEARTAYIKDLHGWLLAWDPVKMETVWKIDHKGPWNG 521 + A + VG ++ P G AWDP + VW++ P Sbjct: 402 NY--IAGTPYVGANVKMYAGPG----------GHRGTFTAWDPAQRRKVWELKEDLPLWS 449 Query: 522 GILATGGDLLFQGLANGEFHAYDATNGSDLYKFDAQSGIIAPPMTY-SVNGKQYVAVEVG 580 G LAT G L+F G +G F A DA +G L++F SGII P++Y +G+QY+A+ G Sbjct: 450 GALATAGGLVFYGTMDGWFKAVDAGSGELLWRFKTGSGIIGQPISYRGPDGRQYIAILSG 509 Query: 581 WGG 583 GG Sbjct: 510 VGG 512 Lambda K H 0.318 0.137 0.439 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: 1629 Number of extensions: 153 Number of successful extensions: 18 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: 742 Length of database: 559 Length adjustment: 38 Effective length of query: 704 Effective length of database: 521 Effective search space: 366784 Effective search space used: 366784 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 (21.7 bits) S2: 54 (25.4 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