Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate WP_007665341.1 BN137_RS16385 c-type cytochrome
Query= reanno::WCS417:GFF2133 (447 letters) >NCBI__GCF_000319285.1:WP_007665341.1 Length = 398 Score = 358 bits (920), Expect = e-103 Identities = 185/384 (48%), Positives = 244/384 (63%), Gaps = 14/384 (3%) Query: 50 VSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFD 109 +SRGEYVAR DC+ACH+ A AP AGG++ ATPLG I++TNITPD + GIG YS DF Sbjct: 21 MSRGEYVARAGDCMACHTAADGAPLAGGVKFATPLGDIYSTNITPDNTHGIGGYSYEDFA 80 Query: 110 RAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNM 169 RA+R GVA G LYPAMPYPSY K+SD+D++ALY + M +KP N SDIPWPL+M Sbjct: 81 RAMREGVAKDGHHLYPAMPYPSYAKMSDEDLRALYEYLMNEVKPQATANRDSDIPWPLSM 140 Query: 170 RWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAG 229 RWP+ +WN +FA + + D+ A WNRGAY+VQGPGHCG+CHTPRG+ EKA DE Sbjct: 141 RWPLGIWNSLFADEKPFTPRADKSAQWNRGAYLVQGPGHCGACHTPRGIGMQEKAFDERD 200 Query: 230 APFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQ 289 FLAG L+GWYAPSLR GL + SE + L+ GR+ HA + G M E NSTQ Sbjct: 201 EQFLAGEELNGWYAPSLR-----GL-KMSEGDLTLLLRDGRSKHAALSGPMDEVVTNSTQ 254 Query: 290 FMQDDDLAAIARYLKSLPG-DPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKG 348 ++ DDD AIA YL SLPG +P + AP + + AA+++ G YA CA+CH +G+G Sbjct: 255 YLSDDDNRAIASYLLSLPGSEPVKTQAP--HLSQAALEN--GHQLYARYCATCHASNGEG 310 Query: 349 QPEWMPPLAGATSALAKESASAINITLNGSQRVVAS-GVPDAYRMPAFREQLSDTEIAEV 407 +P L + A + + + L G + V +P Y MP + LSD + A+V Sbjct: 311 ADYAVPALKDNLTVNADNPLTLLRVVLEGGKTAVTERHLP--YSMPGYGWALSDQDAADV 368 Query: 408 LSYVRSTWGNNGGAVDANAVGKLR 431 +Y+R ++GN+ V + V R Sbjct: 369 TNYIRGSFGNHAAPVTPDQVKDAR 392 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: 600 Number of extensions: 22 Number of successful extensions: 4 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: 398 Length adjustment: 32 Effective length of query: 415 Effective length of database: 366 Effective search space: 151890 Effective search space used: 151890 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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