Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate WP_012386274.1 BIND_RS17085 aldehyde dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >NCBI__GCF_000019845.1:WP_012386274.1 Length = 432 Score = 230 bits (586), Expect = 8e-65 Identities = 148/399 (37%), Positives = 204/399 (51%), Gaps = 24/399 (6%) Query: 25 AWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPL 84 AW P TP A ++F+PALV+RGE +A C ACH+ G PF+GG M T Sbjct: 24 AWRPAIAPITP----PAPSSFDPALVARGEVLAGAGYCSACHTPKGGKPFSGGRPMFTDF 79 Query: 85 GAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALY 144 G I+ATNITPD TGIG +S F RAV GVA G + PA P+ KLS+ D+KALY Sbjct: 80 GTIYATNITPDPKTGIGDWSEEAFRRAVWEGVARDGSHILPAFPFDHLTKLSEQDVKALY 139 Query: 145 AFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQ 204 A+FM +P + IP+P+N+R A W +F + +PD+ WNRGAY+ + Sbjct: 140 AYFMTR-EPVEATAPENTIPFPMNIRLFQAGWKLLFFRPGRFEPRPDKSEEWNRGAYLAE 198 Query: 205 GPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQ 264 G HCG+CHTPR L EK + AGA +D W AP L + N WS ++ Sbjct: 199 GISHCGACHTPRNLLGAEKP-----SATYAGAFIDNWVAPPLDKS-NPSPVPWSRDELYT 252 Query: 265 FLKTGRNA-HAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQR--DGAPWQYQA 321 +L+TG + H G M+ ++ + + D D+ AIA Y + R + +A Sbjct: 253 YLRTGLSRYHGTASGPMSPVVHDGLKLVSDADVRAIATYFADIDQAAARASEETAAVSRA 312 Query: 322 VAA------VQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITL 375 +AA + D A Y CASCH G+ P P LA ++ + + I I L Sbjct: 313 LAASKQGVGLSDDSAAKLYTAACASCHYNGGEINP-LRPDLALNSAVNLDDPTNLIRIIL 371 Query: 376 NGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRST 414 G V G D MPAF SD ++A + +Y+R+T Sbjct: 372 FGVD--VKEGASDLV-MPAFASGFSDADVAHIAAYLRAT 407 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: 597 Number of extensions: 42 Number of successful extensions: 7 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: 432 Length adjustment: 32 Effective length of query: 415 Effective length of database: 400 Effective search space: 166000 Effective search space used: 166000 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 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