Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate N515DRAFT_0703 N515DRAFT_0703 Cytochrome c
Query= BRENDA::C9K502 (472 letters) >FitnessBrowser__Dyella79:N515DRAFT_0703 Length = 429 Score = 278 bits (711), Expect = 3e-79 Identities = 162/409 (39%), Positives = 224/409 (54%), Gaps = 32/409 (7%) Query: 30 DEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTF 89 D LI KGEY+ +GDC +CHT G ++AGG + TP G I + N+TPD G+G ++F Sbjct: 45 DPALIAKGEYLTLVGDCASCHTGQGGARFAGGRVVGTPFGDIPAPNLTPDRETGLGEWSF 104 Query: 90 KEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGVQPIAQKNHPTDISW 149 + F +A+ GV + G LYPA PY S+ ++++DD A++AY + + P+ Q + + Sbjct: 105 EAFRQALHSGVDRHGQFLYPAFPYTSYTKVSRDDALAIFAY-LQSLPPLKQAAKQPGLGF 163 Query: 150 PMSMRWPLSIWRSVF---APAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHIPR-GFGM 205 P ++R L WR+++ D T +P E RG YLV G GHC CH+ R FG Sbjct: 164 PYNVRNTLKAWRALYFREGEYVADSTKSP----EWNRGAYLVQGLGHCNECHVERDSFGG 219 Query: 206 QEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFG 265 SGG + NW AP L GL WS+ D+ LK+G++ AAFG Sbjct: 220 MRSDQSLSGGQI------PVQNWYAPDLSTQANGGLAGWSERDIADLLKTGQSAKGAAFG 273 Query: 266 GMADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDAS---TAQMLDSNNFSGNA 322 MA+VV STQ+ DADLHA+ Y++SL PAR SY+ S T MLD Sbjct: 274 PMAEVVARSTQHLNDADLHAIATYLQSL----PARPRVSYEPSLLDTKPMLDQ------- 322 Query: 323 GAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSA 382 GAK Y E+CA CH DG GVA ++PPL+GN V + +V+ GG P T P Sbjct: 323 GAKVYAERCADCHGRDGQGVAGVYPPLSGNSSVNEPTGINAIRVVLLGGFAPSTQGNPRP 382 Query: 383 VAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLRLDHTPL 431 +MP + L+D +A VV +IR +WGN+AP D+ K R HTP+ Sbjct: 383 YSMPPFAQQLNDADVAAVVTYIRQSWGNQAPL-VQERDVIKYR--HTPI 428 Lambda K H 0.318 0.135 0.431 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: 681 Number of extensions: 49 Number of successful extensions: 6 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: 472 Length of database: 429 Length adjustment: 33 Effective length of query: 439 Effective length of database: 396 Effective search space: 173844 Effective search space used: 173844 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: 51 (24.3 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