Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate PfGW456L13_3925 Putative diheme cytochrome c-553
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3925 Length = 412 Score = 251 bits (641), Expect = 3e-71 Identities = 156/420 (37%), Positives = 221/420 (52%), Gaps = 21/420 (5%) Query: 12 AVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTI 71 A+AVGL A AHA +A +K+GEY+AR DC+ACHT+ G YAGGL I +P GTI Sbjct: 9 ALAVGLAAPVVAAHADDAQ---VKQGEYLARAADCMACHTAPGGAPYAGGLPIVSPFGTI 65 Query: 72 YSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYF 131 Y TNITP +GIG Y EF A+ G R+DGA LYPAMPY S+ + + D A++AY Sbjct: 66 YGTNITPSKEHGIGLYNDDEFFAALTEGKRRDGANLYPAMPYTSYHLIPRADSDAIHAY- 124 Query: 132 MHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGP 191 + V+PI + T +S+P ++R L W ++ K PA G RG+Y+V Sbjct: 125 LKTVEPIERAAPVTSLSFPFNVRLGLMGWNMMYGKDVK-LEPAEGKSEAWKRGQYMVDVL 183 Query: 192 GHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFL 251 GHCG CHTPRG L + D GG+++ ++APSL + G W+ +DL Sbjct: 184 GHCGECHTPRG-------LPGAMQMDKRMTGGILNGYLAPSLLATDLAARG-WNHQDLSS 235 Query: 252 FLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQ 311 FLK G + F M V STQ +D DL AM ++ L PPA Sbjct: 236 FLKHGMSAQGTMFNEMFPVFHNSTQGLSDPDLAAMATFL--LGDQPPAA-----KVLVEV 288 Query: 312 MLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGG 371 LD + S G + Y+ CA CH G G + + GN + ++P ++ ++ DG Sbjct: 289 PLDKLSPSVQRGRQEYLNVCAGCHAPGGEGKPHIAVAMRGNTTLRLEDPRNLVRVIDDGI 348 Query: 372 VLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLRLDHTPL 431 + MP + + L+D+Q+ D++N++R WG + P + D+QKLR D PL Sbjct: 349 GEQKFSGFEHMQPMPGFVDKLNDEQLTDLLNYLRQGWGGQ-PNDLAVNDVQKLRADAPPL 407 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: 585 Number of extensions: 33 Number of successful extensions: 9 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: 412 Length adjustment: 32 Effective length of query: 440 Effective length of database: 380 Effective search space: 167200 Effective search space used: 167200 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