Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate WP_086510868.1 BZY95_RS15845 aldehyde oxidase
Query= reanno::WCS417:GFF2133 (447 letters) >NCBI__GCF_002151265.1:WP_086510868.1 Length = 999 Score = 219 bits (557), Expect = 4e-61 Identities = 139/421 (33%), Positives = 214/421 (50%), Gaps = 27/421 (6%) Query: 4 RRFARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCV 63 RR+ + A AL + ++AW + TP + A + + RG VA DC Sbjct: 565 RRWLKAA---ALTAVAGTAVMAW-PWKGAITPINRPAANL-YSAETIERGRLVAAAGDCA 619 Query: 64 ACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRL 123 ACH+ G AGG TP G +++TN+TPD+ TGIG +S A F+RA+RHG++ G+ L Sbjct: 620 ACHTAEGGQENAGGRAFDTPFGTLYSTNLTPDEETGIGRWSYAAFERAMRHGISRDGKHL 679 Query: 124 YPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSD-IPWPLNMRWPIALWNGVFAP 182 YPA PY ++ K+SD D++ALYA+ M +PA P++ + +P N R +A WN ++ Sbjct: 680 YPAFPYTAFAKISDADMQALYAYLM--AQPAVSAETPANALSFPFNFRPLMAGWNALYHD 737 Query: 183 TATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWY 242 + P Q L+NRGAY+ +G GHC +CH+PR N ++ G LAGA++DGW Sbjct: 738 PNPFEPDPGQSDLYNRGAYLAEGLGHCSACHSPR----NAMGAEQRGEHSLAGAMVDGWE 793 Query: 243 APSLRQDPNTGLGRWSEPQIVQFLKTGRNA-HAVVYGSMTEAFNNSTQFMQDDDLAAIAR 301 AP L + + + WSE + +L+ G ++ H V G M + + + D+ A+A Sbjct: 794 APPLNRLSRSPI-PWSETSLYDYLRHGASSLHGVASGPMAPVVAGLGE-LPEYDVRALAH 851 Query: 302 YLKSLPGDPQRDGAPWQYQA---VAAVQDAP-----GAHTYATRCASCHGLDGKGQ-PEW 352 Y+ P D + A +A Q P G + CASCH +G Sbjct: 852 YVAVQMDAPAGDSETVRADAAVRIATAQSGPAGMEEGERLFEGACASCHMENGTPSFTSA 911 Query: 353 MPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVR 412 LA T+ ++ + I L G V A VP MP F + SD+++ + +Y+R Sbjct: 912 QTSLALNTNLHSQHPDNVIQSILGG---VHADHVPGLGNMPGFADSFSDSQVVTLTAYLR 968 Query: 413 S 413 + Sbjct: 969 A 969 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: 1362 Number of extensions: 80 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: 447 Length of database: 999 Length adjustment: 38 Effective length of query: 409 Effective length of database: 961 Effective search space: 393049 Effective search space used: 393049 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: 54 (25.4 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