Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate BPHYT_RS01060 BPHYT_RS01060 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__BFirm:BPHYT_RS01060 Length = 417 Score = 379 bits (974), Expect = e-110 Identities = 191/405 (47%), Positives = 253/405 (62%), Gaps = 16/405 (3%) Query: 46 EPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSL 105 + AL+ RG Y+A L DC ACH F GGL + TP+G ++ TNITPD +TGIG Y+ Sbjct: 4 DTALIRRGAYLAVLGDCAACHVAKDGKAFVGGLPITTPIGTLYTTNITPDPATGIGNYTP 63 Query: 106 ADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPW 165 +DF+RAVR G+ G +YPAMPYPSY +SDDD++ALYA+FM G+ P + PN S IPW Sbjct: 64 SDFERAVRRGIRRDGSPMYPAMPYPSYAHVSDDDVRALYAYFMHGVAPVDSPNRASGIPW 123 Query: 166 PLNMRWPIALWNGVFAPTATYAAKPDQD-----------ALWNRGAYIVQGPGHCGSCHT 214 PL+MRWP+ W FAP AA D D AL RG Y+V+G HCGSCHT Sbjct: 124 PLSMRWPLTYWRWAFAPKVQPAAHTDIDSATAAGAAHDAALLERGRYLVEGLMHCGSCHT 183 Query: 215 PRGLAFNEKALDEA-GAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAH 273 PRG+ EKAL +A G+ +L+G ++D + A SLR D TGLGRWS+ IV+FL+TGRN Sbjct: 184 PRGVGLQEKALGDADGSDYLSGGVIDHYVANSLRGDDLTGLGRWSQADIVEFLRTGRNPE 243 Query: 274 AVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAVQ----DAP 329 +G M + +S+QF+ D DL A+A YLKSLPG+ + A AA+ A Sbjct: 244 TAAFGGMRDVVQHSSQFLNDTDLLAVATYLKSLPGNHPAGHYAYAAAAGAALAKGDVSAR 303 Query: 330 GAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDA 389 GA Y CA+CH GKG + P LAG AK+ S INI LNG+ V S VP Sbjct: 304 GAIDYLNSCAACHLSSGKGYRDTFPALAGNPVVNAKDPTSLINIVLNGNTEVGTSRVPTQ 363 Query: 390 YRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHT 434 + MP F ++L+D E+A V++++R++WGN+ V+A+ V K+R T Sbjct: 364 FTMPPFGDRLTDAEVANVVTFIRTSWGNHAPDVNADEVAKVRAQT 408 Score = 35.8 bits (81), Expect = 3e-06 Identities = 55/205 (26%), Positives = 82/205 (40%), Gaps = 40/205 (19%) Query: 41 AGATFEPALVSRGEY-VARLSDCVACHSLAG---KAPFAGGLEMATPL--GAIH---ATN 91 AGA + AL+ RG Y V L C +CH+ G + G + + L G I A + Sbjct: 156 AGAAHDAALLERGRYLVEGLMHCGSCHTPRGVGLQEKALGDADGSDYLSGGVIDHYVANS 215 Query: 92 ITPDKSTGIGTYSLADFDRAVRHGVAP-----GGRRLYPAMPYPSYVKLSDDDIKALYAF 146 + D TG+G +S AD +R G P GG R + S L+D D+ A+ A Sbjct: 216 LRGDDLTGLGRWSQADIVEFLRTGRNPETAAFGGMR---DVVQHSSQFLNDTDLLAV-AT 271 Query: 147 FMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGP 206 +++ + P N P G +A A A + + RGA + Sbjct: 272 YLKSL-PGNHP-------------------AGHYAYAAAAGAALAKGDVSARGA--IDYL 309 Query: 207 GHCGSCHTPRGLAFNEKALDEAGAP 231 C +CH G + + AG P Sbjct: 310 NSCAACHLSSGKGYRDTFPALAGNP 334 Score = 26.6 bits (57), Expect = 0.002 Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 5/67 (7%) Query: 41 AGATFEPALVSRGEYVARLSDCVACHSLAGKA-----PFAGGLEMATPLGAIHATNITPD 95 AGA VS + L+ C ACH +GK P G + NI + Sbjct: 291 AGAALAKGDVSARGAIDYLNSCAACHLSSGKGYRDTFPALAGNPVVNAKDPTSLINIVLN 350 Query: 96 KSTGIGT 102 +T +GT Sbjct: 351 GNTEVGT 357 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: 611 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 447 Length of database: 417 Length adjustment: 32 Effective length of query: 415 Effective length of database: 385 Effective search space: 159775 Effective search space used: 159775 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