Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate 3607055 Dshi_0476 Pyrrolo-quinoline quinone (RefSeq)
Query= BRENDA::P18278 (742 letters) >FitnessBrowser__Dino:3607055 Length = 600 Score = 292 bits (748), Expect = 3e-83 Identities = 208/635 (32%), Positives = 296/635 (46%), Gaps = 68/635 (10%) Query: 15 ILAAG-TICAAALPYAAVPARADGQGNTGEAIIHADDHPENWLSYGRTYSEQRYSPLDQI 73 +L +G +CAA + YA + +I D + W Y RYS LD+I Sbjct: 6 LLTSGIALCAATVAYA------------NDDLITQMDDSKQWAIQTGDYKNHRYSELDEI 53 Query: 74 NRSNVGDLKLLGYYTLDTNRGQEATPLVVDGIMYATTNWSKME-ALDAAT-GKLLWQYDP 131 N NVGDL++ ++ RG E +PLV+ MY T + + ALD + GK++W+Y+P Sbjct: 54 NAENVGDLQVAWTFSTGVLRGHEGSPLVIGDTMYVHTPFPNIVYALDLSNEGKIIWKYEP 113 Query: 132 KVPGNIADKGCCDTVNRGAGYWNGKVFWGTFDGRLVAADAKTGKKVWAVNTIPADASLGK 191 K ++ CCDTVNRG Y +GK+F D ++VA DA TG +W V D S+G+ Sbjct: 114 KQDPDVIPVMCCDTVNRGVAYADGKIFLHQADTKVVALDANTGDVLWEVQN--GDPSIGE 171 Query: 192 QRSYTVDGAVRVAKGLVLIGNGGAEFGARGFVSAFDAETGKLKWRFYTVPNNKN---EPD 248 + TV K V++G G EFG RG V+A+D +G+L WR Y++ + + +P+ Sbjct: 172 TNTATV----LPVKDKVIVGISGGEFGVRGHVTAYDINSGELVWRAYSLGPDDDMLVDPE 227 Query: 249 HAA--SDNILMNKAYKTWGPKGAWVRQGGGGTVWDSLVYDPVSDLIYLAVGNGSPWNYKY 306 + I N + +W W+ GGGT W D +L Y GN S WN Sbjct: 228 NTTHLGKPIGENSSLNSW-EGDQWMI--GGGTTWGWYAADMEENLFYYGTGNPSTWNPAQ 284 Query: 307 RSEGIGSNLFLGSIVALKPETGEYVWHFQATPMDQWDYTSVQQIMTLDMPVKGEMRHVIV 366 R G N + +++A +TG W +Q TP D+WDY V + + + GEMR ++ Sbjct: 285 RP---GDNRWTMTVMARDIDTGMAKWFYQMTPHDEWDYDGVNENILTEQEFDGEMRKLLT 341 Query: 367 HAPKNGFFYVLDAKTGEFLSGKNY-VYQNWANGLD-----PLTGRPMYNPDGLYTLNGKF 420 +NG Y +D TGE L + + NW G+D GRP NG+ Sbjct: 342 RFDRNGLAYTMDRVTGELLVAEKFDPVVNWTTGVDMDPNSETYGRPQVVAQYSTAQNGED 401 Query: 421 --WYGI-PGPLGAHNFMAMAYSPKTHLVYIPAHQIPFGYKNQVGGFKPHADSWNVGLDMT 477 GI P LG + AYSPKT + Y+P + + Y+ P S+ G Sbjct: 402 VNTTGICPAALGTKDQQPAAYSPKTQVFYVPTNHVCMDYE-------PFRVSYTAGQPYV 454 Query: 478 KNGLPDTPEARTAYIKDLHGWL---LAWDPVKMETVWKIDHKGPWNGGILATGGDLLFQG 534 L P D HG + +AWD + E +W I K G LAT GD++F G Sbjct: 455 GATLSMYPAP------DSHGGMGNFIAWDNINGEILWSIPEKFSVWSGALATAGDVVFYG 508 Query: 535 LANGEFHAYDATNGSDLYKFDAQSGIIAPPMTYSVNGKQYVAVEVGWGGIYPISMG---- 590 G A A G +LY+F SGII MTY +G+QYV V G GG I + Sbjct: 509 TLEGHLKAVHADTGEELYRFKTPSGIIGNVMTYEHDGRQYVGVLSGVGGWAGIGLAAGLT 568 Query: 591 ----GVGRTSGWTVNHSYIAAFSLDGKAKLPALNN 621 G+G G+ Y A L G+ + AL N Sbjct: 569 NPNDGLGAVGGYAALSDYTA---LGGQLTVFALPN 600 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: 1642 Number of extensions: 125 Number of successful extensions: 11 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: 600 Length adjustment: 38 Effective length of query: 704 Effective length of database: 562 Effective search space: 395648 Effective search space used: 395648 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