Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Ac3H11_3320 Choline dehydrogenase (EC 1.1.99.1)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3320 Length = 562 Score = 355 bits (912), Expect = e-102 Identities = 220/553 (39%), Positives = 293/553 (52%), Gaps = 34/553 (6%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FD +I+G G+AG +LANRLSAD V L+EAG +D IH P+G + +W + Sbjct: 6 FDTIIIGGGTAGALLANRLSADGRHRVLLIEAGRKDDYHWIHIPVGYLYCIGNPRTDWLY 65 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQAL-GNEGWGFDDVLPY 121 T P GL GR PRGK LGG SSINGMIY+RG D++ W L G+ GW +D+ LPY Sbjct: 66 NTEPDTGLNGRTLRYPRGKTLGGCSSINGMIYMRGQARDYDQWAELTGDAGWRWDNALPY 125 Query: 122 FRKSEMH----------------HGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAG 164 FR+ E H HG + G GE V R +AF +A +AG Sbjct: 126 FRRHEDHWRLDQPGSANENFKRLHGNKAT--GSTGEWRVEKQRLRWDVLDAFAHAAQQAG 183 Query: 165 HSYNPDFNGATQEGAGYYDVTIRDGRRWSTATAFLKPVRH-RSNLTVLTHTHVESIVLL- 222 DFNG + EG GY++V + G RW+TA AFL+P + R N + T +V+ Sbjct: 184 IPATDDFNGGSNEGVGYFEVNQKSGWRWNTAKAFLRPTCYGRPNFEMWTSAQAAKLVVET 243 Query: 223 ----GKQATGVQALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPR 278 K+ TGV V +A EVILSAGA SP LL LSGIG AA L GI Sbjct: 244 QPDGSKRCTGVMVWDGQEMVTAQATGEVILSAGAVNSPQLLQLSGIGPAALLRQHGIDVA 303 Query: 279 HELPGVGQNLQDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEA 338 +LPGVG NLQDH + +K L + V K +YA R+GP++ ++ Sbjct: 304 VDLPGVGANLQDHLQIRAVFKVQGVQTLNTMANSLVGKAKIGLEYALKRSGPMSMAPSQL 363 Query: 339 GAFLKTDPGLERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPR 398 GAF ++ P+I+ H ++D LH F+ VC L P S G+V + S D + Sbjct: 364 GAFTRSSADQPYPNIEYHVQPLSLDAFGEPLHSFPAFTASVCNLNPTSRGTVNIKSADFK 423 Query: 399 KAPRIDPNFLAHDDDVATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLR 457 AP I PN+L+ +D R+TR I+AQ +A + + +DE L L Sbjct: 424 TAPAIAPNYLSTPEDRQVAADSLRVTRRIVAQPALAKYRPEEWKPGVQFESDEDLARLAG 483 Query: 458 KRTDTIYHPIGTCKMG--QDEMAVVDSQLRVHG-----IEGLRVVDASIMPTLVGGNTNA 510 TI+HP+GT KMG D MAV+D+Q+RV + GLRVVDA MPT+ GNTN+ Sbjct: 484 DIATTIFHPVGTTKMGLDGDPMAVLDAQMRVRDGRGGVVAGLRVVDAGAMPTITSGNTNS 543 Query: 511 AAIMIAERAAEWI 523 +M+AE+AAEWI Sbjct: 544 PTLMMAEKAAEWI 556 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: 786 Number of extensions: 48 Number of successful extensions: 7 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: 562 Length adjustment: 35 Effective length of query: 491 Effective length of database: 527 Effective search space: 258757 Effective search space used: 258757 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