Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate AO353_22385 AO353_22385 dehydrogenase
Query= BRENDA::Q44002 (739 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22385 Length = 591 Score = 345 bits (884), Expect = 5e-99 Identities = 212/590 (35%), Positives = 304/590 (51%), Gaps = 53/590 (8%) Query: 21 ICAALISGYATMASADDGQGATGEAIIHADDHPGNWMTYGRTYSEQRYSPLDQINRSNVG 80 + A L+SG A A D + I+ +PG +T G QRYSPLD +N +NV Sbjct: 16 LSAMLLSGSALAAVTD-------QDILQDPKNPGQVVTNGLGVQGQRYSPLDILNVNNVK 68 Query: 81 NLKLAWYLDL--DTNRGQEGTPLVIDGVMYATTNWSMMKAVDAATGKLLWSYDPRVPGNI 138 L+ W + RGQ+ P+V DGVMY T ++S + AVDA TGK LW YD R+P +I Sbjct: 69 ELRPVWAFSFGGEKQRGQQAQPMVKDGVMYMTGSYSRVFAVDAHTGKKLWQYDARLPDDI 128 Query: 139 ADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIPPEAELGKQRSYTV 198 + CCD +NRG A ++ V FGT D +L+AL+ TGK+VWS + Y++ Sbjct: 129 --RPCCDVINRGVALYDDLVIFGTLDAKLVALNKDTGKVVWSKKVAD------HKEGYSI 180 Query: 199 DGAPRIAKGRVIIGNGGSEFGARGFVTAFDAETGKVDWRFFTAPNPKNEPDHTASDSVLM 258 AP + G++I G G EFG G + A++ + G++ W T P + + D + Sbjct: 181 SAAPLVVNGKLITGVAGGEFGVVGKIEAYNPKNGELLW---TRPTVEGHMGYVYKDGKAI 237 Query: 259 N------KAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPWNYKYRSEGK 312 +A +TW P W + GG W YDP +L+ G GN +PWN R Sbjct: 238 ENGISGGEAGKTW-PGDLW--KTGGAAPWLGGYYDPETNLLLFGTGNPAPWNSHLRP--- 291 Query: 313 GDNLFLGSIVALKPETGEYVWHFQETPMDQWDFTSVQQIMTLDLPINGETRHVIVHAPKN 372 GDNL+ S +AL P+ G WHFQ TP D WDF V ++++ + G+ A +N Sbjct: 292 GDNLYSSSRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEIKAAATADRN 351 Query: 373 GFFYIIDAKTGEFISGKNYV-YVNWASGLDPKTGRPIYNPDALYTLTGKEWYG-----IP 426 GFFY++D G+FI G +V + WASGLD K GRPIYN + G E G P Sbjct: 352 GFFYVLDRTNGKFIRGFPFVDKITWASGLD-KDGRPIYNEASRPGAPGTEEKGSSVFVAP 410 Query: 427 GDLGGHNFAAMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDSWNLGLDMNK-VGIPDS 485 LG N+ MA++ TGL Y+P+ N+ G D WN G+ K + Sbjct: 411 AFLGAKNWMPMAYNQDTGLFYVPS--------NEWG-----MDIWNEGIAYKKGAAFLGA 457 Query: 486 PEAKQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANGEFHAYD 545 + +D G + A DP+ E WR + P GG+L T G+L+F G G A++ Sbjct: 458 GFTIKPLNEDYIGVLRAIDPKTGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFN 517 Query: 546 ATNGSDLFHFAADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFLGGLAR 595 A G ++ F SG++ P+T+ +G+QYV+V GWGG P + G +A+ Sbjct: 518 AKTGEKVWEFQTGSGVLGSPITWEMDGEQYVSVLSGWGGAVPLWGGEVAK 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: 1825 Number of extensions: 159 Number of successful extensions: 22 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