Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate GFF485 Psest_0490 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::Q0KDL6 (366 letters) >FitnessBrowser__psRCH2:GFF485 Length = 357 Score = 598 bits (1542), Expect = e-176 Identities = 297/363 (81%), Positives = 321/363 (88%), Gaps = 7/363 (1%) Query: 3 AMMKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTVGH 62 AMMKAAVFVEPGRIEL DKPIP+IGPNDAL+RITTTTICGTDVHILKGEYPVA GLT+GH Sbjct: 2 AMMKAAVFVEPGRIELQDKPIPEIGPNDALLRITTTTICGTDVHILKGEYPVAAGLTIGH 61 Query: 63 EPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHGYK 122 EPVG+IEKLGS V GY+EGQRVIAGAICP+F SYA QDG+ SQDG C CHGYK Sbjct: 62 EPVGVIEKLGSNVKGYQEGQRVIAGAICPSFTSYACQDGLPSQDGG-------CSCHGYK 114 Query: 123 ATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENANIR 182 GWRFGN IDGTQAEYVLVPDAQANL P+PDGLTDEQVLMCPDIMSTGF GAE ANI+ Sbjct: 115 PMGGWRFGNTIDGTQAEYVLVPDAQANLAPVPDGLTDEQVLMCPDIMSTGFAGAEAANIK 174 Query: 183 IGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDVVD 242 IGD V +FAQGPIGLCATAGA+L GA+TIIA+DG D RL+IARKMGADV LNFRN DVVD Sbjct: 175 IGDIVVIFAQGPIGLCATAGAKLRGASTIIAVDGVDARLDIARKMGADVTLNFRNVDVVD 234 Query: 243 EVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGLGD 302 EV+KLT GRG DASIEALG Q+TFE +LRVLKPGGTLSSLGVYSSDLTIPL AF AGLGD Sbjct: 235 EVLKLTSGRGADASIEALGLQSTFESALRVLKPGGTLSSLGVYSSDLTIPLGAFHAGLGD 294 Query: 303 HKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLKIA 362 +KI T+LCPGGKERMRRL+NV+ SGRVDLG LVTH+Y LD+I AYDLFANQRDGVLK+A Sbjct: 295 NKIVTSLCPGGKERMRRLLNVVASGRVDLGLLVTHKYALDNITDAYDLFANQRDGVLKVA 354 Query: 363 IKP 365 IKP Sbjct: 355 IKP 357 Lambda K H 0.320 0.138 0.408 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: 590 Number of extensions: 15 Number of successful extensions: 2 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: 366 Length of database: 357 Length adjustment: 29 Effective length of query: 337 Effective length of database: 328 Effective search space: 110536 Effective search space used: 110536 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 (21.8 bits) S2: 49 (23.5 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