Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 207896 DVU2405 alcohol dehydrogenase, iron-containing
Query= BRENDA::P0DJA2 (383 letters) >MicrobesOnline__882:207896 Length = 393 Score = 388 bits (997), Expect = e-112 Identities = 200/383 (52%), Positives = 262/383 (68%), Gaps = 6/383 (1%) Query: 6 FYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINSAVY 65 F+IP V +G G+ + + + G LIV+D + K+G++KQ+ DLL A + +VY Sbjct: 10 FFIPRVTLIGIGASKAIPEKIKALGGSKPLIVTDMGIVKAGILKQITDLLDAAKMAYSVY 69 Query: 66 DGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEGIDK 125 D +PNPT V +G+ + K N D +I+LGGGS HDC K I LV NGG++ D+EG+DK Sbjct: 70 DETIPNPTDDNVHKGVDVYKKNKCDSLITLGGGSSHDCGKGIGLVVANGGKIHDFEGVDK 129 Query: 126 SKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPK 185 S + P +++NTTAGTASEMTRFCIITD R VKMAIVD VTP ++++DPLLM+GMP Sbjct: 130 STQRMPPYLAVNTTAGTASEMTRFCIITDTSRKVKMAIVDWRVTPNIALDDPLLMLGMPP 189 Query: 186 GLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAY 245 LTAATGMDALTHA EAY ST ATP+TDACA +A ++IA L+ A NG+D+ ARE M + Sbjct: 190 ALTAATGMDALTHAVEAYVSTIATPMTDACAEQAITLIATFLRRAVANGQDLEARERMCF 249 Query: 246 AQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKDVGV 305 AQ+LAGMAFNNASLG+VHAMAHQLGG+Y+LPHG CNA+LLPHV +N R + Sbjct: 250 AQYLAGMAFNNASLGHVHAMAHQLGGFYDLPHGECNAILLPHVSKFNLIAKLDRYARIAQ 309 Query: 306 AMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELG------AKKEDVPLLADHALK 359 MG +IA L +E AE I A++ L+ +GIPA L LG K D+ ++ +A K Sbjct: 310 LMGENIAGLSTREAAERAISAIKCLSTDVGIPAGLVALGKRYGKDVKAADIAIMTKNAQK 369 Query: 360 DACALTNPRQGDQKEVEELFLSA 382 DAC LTNPR +V ++ +A Sbjct: 370 DACGLTNPRCPTDADVAAIYEAA 392 Lambda K H 0.316 0.132 0.373 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: 437 Number of extensions: 19 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: 383 Length of database: 393 Length adjustment: 30 Effective length of query: 353 Effective length of database: 363 Effective search space: 128139 Effective search space used: 128139 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 (21.6 bits) S2: 50 (23.9 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