Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate Ac3H11_2872 Putative diheme cytochrome c-553
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2872 Length = 426 Score = 273 bits (698), Expect = 8e-78 Identities = 154/423 (36%), Positives = 220/423 (52%), Gaps = 10/423 (2%) Query: 12 WLALPCLVAAGLLAWYVTREPATPFEQEQAGATFE--PALVSRGEYVARLSDCVACHSLA 69 W L A G+ A V E A T + PALV RGEY+AR+ +C+ACH+ Sbjct: 6 WTISCALAALGMAAAAVVTLNLRGEEPLPATETLQSTPALVQRGEYLARVGNCMACHTTQ 65 Query: 70 GKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPY 129 G APFAGG + TP G +H++N+TPDK+ GIG+++ A+F RA+ HG + GR LYPA PY Sbjct: 66 GGAPFAGGRGIETPFGVVHSSNLTPDKAQGIGSWTSAEFWRAMHHGRSKDGRLLYPAFPY 125 Query: 130 PSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAK 189 P+Y +++ +D A++A ++Q +PN + +P N + + +W +F + Sbjct: 126 PNYTQVTREDSDAIFA-YLQSQPAVAEPNRAHALRFPYNTQAALGVWRALFFTPGAPQPE 184 Query: 190 PDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGAL-LDGWYAPSLRQ 248 Q A +NRGAY+V G GHC +CHTPR N F G + + WYAP+L Sbjct: 185 ATQSAEYNRGAYLVNGLGHCTACHTPR----NALGATTDAKAFTGGLIPVQNWYAPALNA 240 Query: 249 DPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPG 308 G+ W +V LKTG V G M E S Q + D D A+A YL++LP Sbjct: 241 AHEAGVKEWKTDDVVALLKTGVAPQGSVLGPMAEVVFRSAQHLSDADARAMAVYLQALPQ 300 Query: 309 DPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESA 368 R A +A+ A GA Y CA CHG G+G+P P LAG + + Sbjct: 301 QEHRALAAGAAPPASAL--ARGAKVYEQHCAQCHGDQGQGEPGAFPALAGNRAVTLADPT 358 Query: 369 SAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVG 428 + + + L G +G P + MP F++ LSD +IA V + VR++WGN V V Sbjct: 359 NLVRVVLQGGYLPATAGNPRPHGMPPFQQLLSDEDIAAVTTLVRNSWGNRAPGVGTIEVY 418 Query: 429 KLR 431 + R Sbjct: 419 RAR 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: 640 Number of extensions: 40 Number of successful extensions: 5 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: 426 Length adjustment: 32 Effective length of query: 415 Effective length of database: 394 Effective search space: 163510 Effective search space used: 163510 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