Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate Ac3H11_3427 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3427 Length = 1243 Score = 242 bits (617), Expect = 6e-68 Identities = 155/435 (35%), Positives = 216/435 (49%), Gaps = 51/435 (11%) Query: 4 RRFARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCV 63 R A AG +A+ A LL W R P Q + + A + RG +A DC Sbjct: 813 RALALVAGGIAM----GAALLGW---RPSIAPVVQTVGASVYNAATIERGRLLAAAGDCA 865 Query: 64 ACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRL 123 CH+ G P GG M TP G I+ TN+TPD TGIG +S + F RA+R G++ GG+ L Sbjct: 866 VCHTAPGGTPNTGGRAMETPFGKIYTTNLTPDAETGIGQWSFSAFQRAMREGISQGGKHL 925 Query: 124 YPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIP-SDIPWPLNMRWPIALWNGVFAP 182 YPA PY S+ K+SDDD+ ALYA+ M +PA + +P +++ +P ++R +A WN +F Sbjct: 926 YPAFPYTSFAKMSDDDLTALYAYLM--AQPAVRAEVPKTELTFPFSVRPLMAGWNALFHD 983 Query: 183 TATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWY 242 + P + WNRGAY+VQG GHCG+CHTPR N + GA FL+GA++DGW Sbjct: 984 ATPFKPDPTRPPEWNRGAYLVQGVGHCGACHTPR----NALGAELGGAAFLSGAMIDGWE 1039 Query: 243 APSLRQDPNTGLGR----WSEPQIVQFLKTGRN-AHAVVYGSMTEAFNNSTQFMQDDDLA 297 AP+L TGL + W+ + +L+ G + H G M + DDD+ Sbjct: 1040 APAL-----TGLSKAPVPWTADALYGYLRHGHSPQHGSASGPMAPVVRELAH-LPDDDIR 1093 Query: 298 AIARYLKSLP---------GDPQRDGAPWQYQAVA-AVQDAPGAHTYATRCASCHGLDGK 347 A+A YL S DPQ+ QA A A Q + CA+CH DG Sbjct: 1094 AMASYLASFTAAEAATQPVSDPQQRAQTAVAQAAALAPQPGQAQRLFDGACAACHH-DGD 1152 Query: 348 GQPEWMPPLAGATSALAKES-------ASAINITLNGSQRVVASGVPDAYRMPAFREQLS 400 G P L G LA S + + + ++G + A D MP F LS Sbjct: 1153 G-----PKLLGVNVPLALNSNLHSDRPDNLLQVIVHGIREPAAR---DIGFMPGFGHALS 1204 Query: 401 DTEIAEVLSYVRSTW 415 D +I E+ Y+R + Sbjct: 1205 DAQITELAGYMRQRY 1219 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: 1661 Number of extensions: 95 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: 1243 Length adjustment: 40 Effective length of query: 407 Effective length of database: 1203 Effective search space: 489621 Effective search space used: 489621 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: 55 (25.8 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