Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 8499551 DvMF_0321 iron-containing alcohol dehydrogenase (RefSeq)
Query= BRENDA::Q09669 (422 letters) >FitnessBrowser__Miya:8499551 Length = 393 Score = 392 bits (1006), Expect = e-113 Identities = 204/388 (52%), Positives = 264/388 (68%), Gaps = 12/388 (3%) Query: 46 VSAFYIPSFNLFGKGCLAEAAKQIKMSGFKNTLIVTDPGIIKVGLYDKVKALLEEQSITV 105 V F+IPS L G G ++IK G LIVTD GI+K G+ ++ LL+ + Sbjct: 7 VYGFFIPSVTLIGIGASKAIPEKIKALGGSKPLIVTDMGIVKAGILKQITDLLDAAKMAY 66 Query: 106 HLYDGVQPNPTVGNVNQGLEIVKKENCDSMVSIGGGSAHDCAKGIALLATNGGKIADYEG 165 +YD PNPT NV++G+E+ KK CDS++++GGGS+HDC KGI L+ NGGKI D+EG Sbjct: 67 SVYDETIPNPTDDNVHKGVEVYKKNKCDSLITLGGGSSHDCGKGIGLVIANGGKIHDFEG 126 Query: 166 VDKSSKPQLPLIAINTTAGTASEMTRFAIITEETRHIKMAIIDKHTMPILSVNDPETMYG 225 VDKS KP P +A+NTTAGTASEMTRF IIT+ +R +KMAI+D P ++++DP M G Sbjct: 127 VDKSFKPMPPYVAVNTTAGTASEMTRFCIITDTSRKVKMAIVDWRVTPSIALDDPLLMMG 186 Query: 226 LPPSLTAATGMDALTHAVEAYVSTAANPITDACAVKCIELVNKYLKRAVDNGKDEEARDN 285 +PP+LTAATGMDALTHAVEAYVST A P+TDACA + I L+ +L+RAV NG+D EAR+ Sbjct: 187 MPPALTAATGMDALTHAVEAYVSTIATPMTDACAEQAITLIATFLRRAVANGRDIEARER 246 Query: 286 MAYAEFLGGMAFNNASLGYVHAMAHQLGGFYGIPHGVCNAVLLAHVQKFN-----SRDPR 340 M +A++L GMAFNNASLG+VHAMAHQLGGFY +PHG CNA+LL HV +FN R R Sbjct: 247 MCFAQYLAGMAFNNASLGHVHAMAHQLGGFYDLPHGECNAILLPHVSQFNLIAKLDRFAR 306 Query: 341 ANARLGDIAFHLGCEEHTAEAALDRISQLVLEVKIRPHLVDLG------VKEKDFDVLVD 394 +G+ L + AE A+ I +L +V I LV LG VK KD ++ Sbjct: 307 IAELMGENISGLSVRD-AAEKAICAIKRLSADVGIPAGLVALGKRYGKDVKAKDIAIMTK 365 Query: 395 HAMKDACGATNPIQPTHDEVKAIFKSAM 422 +A KDACG TNP PT +V AI+++AM Sbjct: 366 NAQKDACGLTNPRCPTDADVAAIYEAAM 393 Lambda K H 0.319 0.134 0.390 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: 485 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: 422 Length of database: 393 Length adjustment: 31 Effective length of query: 391 Effective length of database: 362 Effective search space: 141542 Effective search space used: 141542 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: 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