Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate RR42_RS13625 RR42_RS13625 4-hydroxybenzoyl-CoA reductase
Query= SwissProt::Q4J6M6 (281 letters) >FitnessBrowser__Cup4G11:RR42_RS13625 Length = 288 Score = 134 bits (336), Expect = 3e-36 Identities = 85/275 (30%), Positives = 148/275 (53%), Gaps = 4/275 (1%) Query: 6 FSYVRAESLQEALKFLEG-NDNTRPLAGGQSLIPMLKLRVLSPDYILDINRLNELNYVKT 64 F ++ S+ EA + L D R +AGG +L+ ++ R+L P +++ + +L+ L ++ Sbjct: 4 FEFLEPGSVPEASRMLADLGDECRVIAGGTALMLGMRQRMLMPTHLVSLGQLDALRKIEF 63 Query: 65 S-LNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTIGDMQVRNMGTIGGAISNADPASD 123 G+ IGAL + + + +V++ P++ + + QVRN GTIGG + ADPA+D Sbjct: 64 DPRTGLRIGALALHAQVARSPLVQAHYPMLASMAGRVANPQVRNQGTIGGNLCYADPATD 123 Query: 124 MPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDTNKGELVTQIEVPVL-DGYKTVYK 182 P L AL A ++L+ SG R ++ F +TT E+VT+I +P L Y Sbjct: 124 PPGCLMALGAQVVLAGRSGERVLEMEAFLVDYYTTALEPDEIVTEIRIPALAPDALGHYA 183 Query: 183 KVVRRAGDY-ALASVALAIKLKGNEIEDIKLAYGGVHDKPFRAMEVEKNVIGKKLNDDLV 241 + +R A ++ LASV+L + G + +LA G P R E + GK + ++ Sbjct: 184 RFLRTAAEHRPLASVSLLARRTGATCIEARLAVGASTPIPARLRRAEAFLAGKAVTPEVA 243 Query: 242 KDIASKVSSQINPPSDHRGSSWYRREVVKVLTMKA 276 + A V++ I+P SD RG++ YRRE+V+ + ++ Sbjct: 244 AEAADIVAADIDPVSDMRGNADYRREMVRTVARRS 278 Lambda K H 0.316 0.134 0.372 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: 174 Number of extensions: 11 Number of successful extensions: 2 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: 281 Length of database: 288 Length adjustment: 26 Effective length of query: 255 Effective length of database: 262 Effective search space: 66810 Effective search space used: 66810 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 (21.6 bits) S2: 47 (22.7 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