Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate RR42_RS32135 RR42_RS32135 alcohol dehydrogenase
Query= BRENDA::Q44002 (739 letters) >FitnessBrowser__Cup4G11:RR42_RS32135 Length = 733 Score = 573 bits (1476), Expect = e-167 Identities = 309/725 (42%), Positives = 433/725 (59%), Gaps = 45/725 (6%) Query: 7 GKRRSLSR---TLTAGTICAALISGYAT----MASADDGQGAT----GEAIIHADDHPGN 55 G + LSR L AG +L + A +ASAD + T G I + Sbjct: 20 GNQAGLSRKLAVLVAGLAAFSLAAAQARPPVKVASADHIRSVTRSVDGAFIEGNAAKTPD 79 Query: 56 WMTYGRTYSEQRYSPLDQINRSNVGNLKLAWYLDLDTNRGQEGTPLVIDGVMYATTNWSM 115 W +YG Y+E R+S L QIN NV +L LAW DL++ RG E TPLV++G+MY + +WS+ Sbjct: 80 WPSYGLDYAETRFSRLSQINADNVKDLGLAWSYDLESTRGVEATPLVVNGIMYVSASWSV 139 Query: 116 MKAVDAATGKLLWSYDPRVPGNIADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTG 175 + A+D +GK +W++DP+V +I KGCCD VNRG A + GKV+ ++DGRLIALDA TG Sbjct: 140 VHAIDTRSGKRIWTFDPKVDKSIGYKGCCDVVNRGVALYQGKVFVASYDGRLIALDAGTG 199 Query: 176 KLVWSVNTIPPEAELGKQRSYTVDGAPRIAKGRVIIGNGGSEFGARGFVTAFDAETGKVD 235 + +W +TI + + SYT+ GAPR+ KG+VIIGNGG+E+G RG++TA+DA TG+ Sbjct: 200 RKLWEKDTI-----IDRTHSYTITGAPRVFKGKVIIGNGGAEYGVRGYITAYDAATGEQK 254 Query: 236 WRFFTAPNPKNEPDHTASDSVLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYL 295 WR+FT P +P S M KA +TW P G + GGGGT WD++ +DP +L+Y+ Sbjct: 255 WRWFTVPGDPGKPFEDES----MAKAAKTWDPAGKYWEAGGGGTAWDTLAFDPELNLMYV 310 Query: 296 GVGNGSPWNYKYRSEGKGDNLFLGSIVALKPETGEYVWHFQETPMDQWDFTSVQQIMTLD 355 G GNGSPW+ RS GDNL+L SIVAL P+TG+YVWH+QETP D WD+TS Q ++ D Sbjct: 311 GTGNGSPWSRSKRSPAGGDNLYLASIVALDPDTGKYVWHYQETPGDNWDYTSTQPMILAD 370 Query: 356 LPINGETRHVIVHAPKNGFFYIIDAKTGEFISGKNYVYVNWASGLDPKTGRPIYNPDALY 415 L I G+ R VI+HAPKNGFF++ID G+FIS KN+V V WASG D + GRPI P+A Sbjct: 371 LNIGGKARKVILHAPKNGFFFVIDRTNGQFISAKNFVDVTWASGYD-QNGRPIELPEA-- 427 Query: 416 TLTGKEWYGIPGDLGGHNFAAMAFSPKTGLVYIPAQQVPFLYTNQ----VGGFTPHPDSW 471 T K + IPG G HN+ M+F+P+TGLVY+PAQ VP + G P Sbjct: 428 RATDKPYDAIPGPYGAHNWHPMSFNPQTGLVYLPAQHVPLNLMDDKNWTFNGKQPGQPHG 487 Query: 472 NLGLDMNKVGIPDSPEAKQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDL 531 N+G + K + P A + F G ++AWDP +Q W + PWNGG L T G+L Sbjct: 488 NVGWNTAKF-LNAEPPASKPF-----GRLIAWDPVQQKAVWTQEQVSPWNGGTLTTAGNL 541 Query: 532 LFQGLANGEFHAYDATNGSDLFHFAADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFLG 591 +FQG A+G F AY+A G+ L+ +G+IA PV+YL +GKQYV+V VGWGG+Y Sbjct: 542 VFQGTADGRFIAYNAATGAKLWESPTGTGVIAAPVSYLVDGKQYVSVAVGWGGVY----- 596 Query: 592 GLARTSGWTVNHSRIIAFSLDGKSGPLPKQNDQGFLPVKPPAQFDSKRTDNGYFQFQTYC 651 G A+ + + F++ GK+ P+P + ++D G + + C Sbjct: 597 GQAQRATERQGPGTVYTFAVGGKA-PMPAFVQYRAGELLSGVKYDPANVAAGTALYVSNC 655 Query: 652 AACHG-DNAEGAGVLPDLRWSGS--IRHEDAFYNVVGRGALTAYGMDRFDGNMNPTEIED 708 CHG + G +P+L + + I++ D F + +G A GM F G ++ ++E Sbjct: 656 VLCHGVPGVDRGGNIPNLGYMNTAYIQNLDKF---IFKGPAMARGMPDFTGKLSADDVEK 712 Query: 709 IRQFL 713 I+ F+ Sbjct: 713 IKAFI 717 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: 2107 Number of extensions: 154 Number of successful extensions: 14 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: 733 Length adjustment: 40 Effective length of query: 699 Effective length of database: 693 Effective search space: 484407 Effective search space used: 484407 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: 55 (25.8 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