Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate GFF3218 HP15_3160 quinoprotein alcohol dehydrogenase
Query= BRENDA::Q44002 (739 letters) >FitnessBrowser__Marino:GFF3218 Length = 591 Score = 377 bits (967), Expect = e-108 Identities = 222/580 (38%), Positives = 303/580 (52%), Gaps = 45/580 (7%) Query: 32 MASADDGQGATGEAIIHADDHPGNWMTYGRTYSEQRYSPLDQINRSNVGNLKLAWYLDLD 91 MA + T E II+ P + ++YG QRYS L+ +N SNV L+ AW Sbjct: 17 MAVSYGAHAVTDEDIINDHKTPEDIVSYGMGTQGQRYSILEDLNTSNVQYLQPAWAFSFG 76 Query: 92 TN--RGQEGTPLVIDGVMYATTNWSMMKAVDAATGKLLWSYDPRVPGNIADKGCCDTVNR 149 + RGQE PL+ DGVMY T ++S + A+DA TG+ +W YD R+P I CCD VNR Sbjct: 77 SEKMRGQESQPLIKDGVMYVTASYSRIYAIDARTGEEIWQYDARLPDGIMP--CCDVVNR 134 Query: 150 GAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIPPEAELGKQRSYTVDGAPRIAKGRV 209 GAA + KV FGT D +L+AL+ TGK +W I A+ Q Y + AP + KG+V Sbjct: 135 GAAIYGDKVIFGTLDAKLVALNKDTGKPMW----IKKVADY--QAGYAITAAPMVIKGKV 188 Query: 210 IIGNGGSEFGARGFVTAFDAETGKVDWRFFTAPNPKNEPDHTASDS------VLMNKAYQ 263 I G G EFG G V A+DA TG + W T P + + D + KA Sbjct: 189 ITGVSGGEFGIVGKVEAYDANTGDLVW---TRPTVEGHMGYVYKDGKKIENGISGGKAGV 245 Query: 264 TWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPWNYKYRSEGKGDNLFLGSIVA 323 TW P W + GG W YDP D ++ G GN +PWN R GDNLF S +A Sbjct: 246 TW-PGEMW--KNGGAATWLGGTYDPDTDSLFFGTGNPAPWNSHLRP---GDNLFSSSRLA 299 Query: 324 LKPETGEYVWHFQETPMDQWDFTSVQQIMTLDLPINGETRHVIVHAPKNGFFYIIDAKTG 383 + P+ G WHFQ TP D WD+ V ++++ D NG+T A +NGFFY+++ + G Sbjct: 300 IDPDDGSIKWHFQTTPNDGWDYDGVNELISFDYEENGKTVKAAATADRNGFFYVLNRENG 359 Query: 384 EFISGKNYV-YVNWASGLDPKTGRPIY-------NPDALYTLTGKEWYGIPGDLGGHNFA 435 +FI G +V + WA GLDPKTGRPIY NP + G+ P LGG N+ Sbjct: 360 DFIRGFPFVDKITWAEGLDPKTGRPIYAEGGRPGNPADMEGGKGEMVLAQPAFLGGKNWM 419 Query: 436 AMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDSWNLGLDMNKVGIPDSPEAKQAFVKD 495 MAFS +TGL Y+P+ + N+ P S+ G G P D Sbjct: 420 PMAFSQQTGLFYVPSNEWSMDIWNE-------PVSYKKGAAFLGAGFTIKPAND-----D 467 Query: 496 LKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANGEFHAYDATNGSDLFHF 555 G + A DP+ E WR ++ P GG++ T G L+F G G A+DA G +L+ F Sbjct: 468 YIGVLRAMDPKTGEEVWRYENTAPLWGGVMTTAGGLVFTGTPEGHLKAFDAKTGEELYRF 527 Query: 556 AADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFLGGLAR 595 SG++ P+T+ +G+QYV+V GWGG P + G +A+ Sbjct: 528 NTGSGVVGTPITWTMDGEQYVSVASGWGGAVPLWGGEVAK 567 Lambda K H 0.318 0.137 0.440 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: 1794 Number of extensions: 164 Number of successful extensions: 21 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: 739 Length of database: 591 Length adjustment: 38 Effective length of query: 701 Effective length of database: 553 Effective search space: 387653 Effective search space used: 387653 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