Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate RR42_RS10775 RR42_RS10775 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Cup4G11:RR42_RS10775 Length = 434 Score = 362 bits (929), Expect = e-104 Identities = 188/437 (43%), Positives = 250/437 (57%), Gaps = 30/437 (6%) Query: 4 RRFARTAGWLAL---PCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLS 60 RRF+ T + L PC AA + GA A V RG Y+A+++ Sbjct: 6 RRFSATVAFAVLLLAPCFAAAA----------------DAPGA----AQVERGRYLAKVA 45 Query: 61 DCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGG 120 +C ACH+ G APFAGGL + T +G +++TNITPD +GIG YS +FDRA+R GVA G Sbjct: 46 NCAACHTSVGGAPFAGGLPLKTGVGTVYSTNITPDVDSGIGAYSFEEFDRALREGVARHG 105 Query: 121 RRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVF 180 +RLYPAMPYPSY +L++ D++ALYA+ +K Q ++ WP MRW + +WN +F Sbjct: 106 KRLYPAMPYPSYARLAEPDVQALYAYLRTEVKAVRQATAEPEMRWPFGMRWLLRVWNWLF 165 Query: 181 APTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDG 240 + A Q WNRGAY+VQ HCG+CHTPRG+ EK LDE FLAGA ++G Sbjct: 166 LESGPVPANAGQSVEWNRGAYLVQAVAHCGACHTPRGMLMAEKGLDERSRHFLAGASVEG 225 Query: 241 WYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIA 300 W + +LR DP TGLG WS I ++L TGRNAHA +G M+E +STQFM DL A+A Sbjct: 226 WASTNLRGDPRTGLGTWSREDIAEYLHTGRNAHATSFGPMSEVIASSTQFMTRPDLDAVA 285 Query: 301 RYLKSLPGDPQRDGAPWQYQAVAAVQ------DAPGAHTYATRCASCHGLDGKGQPEWMP 354 YLKS+PG + D P+ Y A A DA GA YA C CHG +GKG P Sbjct: 286 VYLKSVPG-ARSDETPYAYDAHTADALAQGRFDATGARQYAEFCMPCHGANGKGFARVFP 344 Query: 355 PLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRST 414 PLAG + + + +S N+ L+G+ Y MP + L + E+A VL+++R+ Sbjct: 345 PLAGNPTVVDPDPSSLANLLLDGAVTAHVGTAATDYHMPGYGWTLDNQELANVLTFIRTG 404 Query: 415 WGNNGGAVDANAVGKLR 431 WGN V V R Sbjct: 405 WGNQASQVKEATVAARR 421 Lambda K H 0.318 0.133 0.423 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: 615 Number of extensions: 28 Number of successful extensions: 3 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: 447 Length of database: 434 Length adjustment: 32 Effective length of query: 415 Effective length of database: 402 Effective search space: 166830 Effective search space used: 166830 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