Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate HSERO_RS23855 HSERO_RS23855 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__HerbieS:HSERO_RS23855 Length = 543 Score = 507 bits (1305), Expect = e-148 Identities = 265/531 (49%), Positives = 344/531 (64%), Gaps = 10/531 (1%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPT--RHVNW 60 FDY+IVG GSAG LA RLS DP ++VCLLEAG + S L+ TP + A+LP + NW Sbjct: 3 FDYVIVGGGSAGATLAARLSEDPRISVCLLEAGGQGDSLLVRTPAAVVAMLPGYGKLNNW 62 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 A +TTPQPGL GR GYQPRG+ LGGSS+IN M+Y+RG + D++ W G GW ++ VLP Sbjct: 63 ALQTTPQPGLNGRRGYQPRGRALGGSSAINAMLYVRGQRQDYDGWAQAGCPGWDWESVLP 122 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGA 179 YF+++E + G+ +HG G L VS NR + AF+E+ GH DFN EG Sbjct: 123 YFKRAENNVRGADAWHGASGPLQVSEQNRPRPITRAFIEAGQARGHRLCQDFNTGDNEGV 182 Query: 180 GYYDVT-----IRDGRRWSTATAFLKPVR-HRSNLTVLTHTHVESIVLLGKQATGVQALI 233 G Y VT G R S A A+L PV R NL+VL + ++ GK+A GV Sbjct: 183 GLYQVTQFHTPAHRGERCSAAAAYLHPVMGQRPNLSVLRQVRAQRLLFEGKRAIGVAYRQ 242 Query: 234 KGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHAD 293 + +RA +EVI++AGAFGSP LL LSG+G + ++ P GIA H LPGVGQNLQDH D Sbjct: 243 QQGDAQVRAAREVIIAAGAFGSPQLLQLSGVGRSDDILPHGIALHHPLPGVGQNLQDHLD 302 Query: 294 VVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDI 353 + + DT G + GG+++ + + RH G +A+ AE AFLKT P L+RPDI Sbjct: 303 FTQGWTTRDTDNFGLGVVGGLRLLGQLLPWKRHGEGLIATPFAEGAAFLKTRPELDRPDI 362 Query: 354 QLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDD 413 QLH I VDDH RKLH G+GFS H+C+LRP S G VGL S DP P IDP +L+ D Sbjct: 363 QLHFCIAIVDDHARKLHAGYGFSLHMCMLRPHSRGRVGLQSADPMADPLIDPGYLSDPRD 422 Query: 414 VATLLKGYRITRDIIAQTPMASFGLRDMYSA-GLHNDEQLIELLRKRTDTIYHPIGTCKM 472 +AT++ G R+ R I+ P+ + R+++ +D Q ++R R DTIYHP GTC+M Sbjct: 423 LATMIDGARMARQIVMTEPLRHYCRRELFGGRDDMDDAQWESMIRHRADTIYHPAGTCRM 482 Query: 473 GQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 G+D MAVVD+QLRVHG++GLRVVDAS+MPTLV GNTNA IMIAE+AA+ I Sbjct: 483 GEDAMAVVDAQLRVHGLQGLRVVDASVMPTLVSGNTNAPTIMIAEKAADMI 533 Lambda K H 0.319 0.137 0.419 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: 931 Number of extensions: 47 Number of successful extensions: 5 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: 526 Length of database: 543 Length adjustment: 35 Effective length of query: 491 Effective length of database: 508 Effective search space: 249428 Effective search space used: 249428 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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