Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate AZOBR_RS04080 AZOBR_RS04080 cytochrome C
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__azobra:AZOBR_RS04080 Length = 288 Score = 105 bits (263), Expect = 1e-27 Identities = 89/305 (29%), Positives = 143/305 (46%), Gaps = 46/305 (15%) Query: 11 GAVAVGLLAGTSLAHA--QNADEDLIKKGEYVAR-LGDCVACHTS------LNGQKYAGG 61 G+VA L+ +A A + E +++G + + C CHT + G++ AGG Sbjct: 8 GSVAACLMLSGMIATAGAETPPESPVERGRALVNGIVACGNCHTPQGPNGPVAGRELAGG 67 Query: 62 LSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQ 121 T Y++NITPDP GIG +T ++ A+R G R DG+ + P MP+ + ++ Sbjct: 68 TPFVEEPFTAYASNITPDPETGIGRWTDEQLIAAIREGRRPDGSLIGPPMPFGFYRGLSD 127 Query: 122 DDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEI 181 D++A+ AY + V P+ P S +R P + P G+ AEI Sbjct: 128 GDLRAIVAY-LRSVPPVRHS-------------VPKSEYRMAL---PAAYGPPVGSVAEI 170 Query: 182 AR------GEYLVTGPGHCGACHTPR-GFGMQEKALDASGGPDFLGGGGVIDNWIAPSLR 234 R G Y+ GHC CHTP G + +GG +F G G N ++ ++ Sbjct: 171 PRTDPVTYGAYMAGPLGHCMECHTPMLPDGRLDMTRMGAGGRNFTGPWG---NAVSRNIT 227 Query: 235 NDPVLGLGRWSDEDLFLFLKSG-RTDHSAAFGGMADVVGWSTQYY---TDADLHAMVKYI 290 D GLG W+D ++ + G R D ++ +G+ YY +D +L A+V Y+ Sbjct: 228 QDKEHGLGGWTDAEIRKAITEGVRPDGHR----LSPPMGY--HYYKSMSDGELGALVAYL 281 Query: 291 KSLPP 295 ++LPP Sbjct: 282 RTLPP 286 Score = 64.3 bits (155), Expect = 5e-15 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 5/119 (4%) Query: 178 DAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDP 237 ++ + RG LV G CG CHTP+G + +GG F+ A ++ DP Sbjct: 30 ESPVERGRALVNGIVACGNCHTPQGPNGPVAGRELAGGTPFVEEPFTA---YASNITPDP 86 Query: 238 VLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPV 296 G+GRW+DE L ++ GR + G + + +D DL A+V Y++S+PPV Sbjct: 87 ETGIGRWTDEQLIAAIREGRRPDGSLIGPPMPFGFY--RGLSDGDLRAIVAYLRSVPPV 143 Lambda K H 0.318 0.135 0.430 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: 471 Number of extensions: 34 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 472 Length of database: 288 Length adjustment: 30 Effective length of query: 442 Effective length of database: 258 Effective search space: 114036 Effective search space used: 114036 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: 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