Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate Ac3H11_4900 Putative amino acid ABC transporter, permease protein
Query= TCDB::P48244 (228 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4900 Length = 217 Score = 100 bits (249), Expect = 2e-26 Identities = 74/224 (33%), Positives = 115/224 (51%), Gaps = 18/224 (8%) Query: 3 TLWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNT 62 +LW L LL A W T+ L++ + IG + G +L +R+S V+ + AY+ + T Sbjct: 5 SLWDILRNLLLAARW-TVSLSLIAFIGGGLVGLLLLVLRLSKVRGVDRAVGAYVQVFQGT 63 Query: 63 PLTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINT 122 PL L+ LF ++ G+ L G ++S + A + LYTS ++ E R + + Sbjct: 64 PL-LMQLFLAY-----FGIALFGIKTSPWTA------AAVALTLYTSAYLTEIWRGCVAS 111 Query: 123 VHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASL 182 + GQ EAA+SL FG R ++ PQA+R A+ P L+ + K T +ASVIG E Sbjct: 112 IPKGQWEAAQSLAFNFGEQLRHVVLPQALRIAVPPTVGFLVQVIKGTALASVIGFVE--- 168 Query: 183 LMKA--TIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224 L KA I N F+V+A A+ + +L P+ L L +L Sbjct: 169 LTKAGSMISNATYKPFLVYACVALLYFVLCFPVSLVAQSLERKL 212 Lambda K H 0.327 0.139 0.397 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: 116 Number of extensions: 6 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: 228 Length of database: 217 Length adjustment: 22 Effective length of query: 206 Effective length of database: 195 Effective search space: 40170 Effective search space used: 40170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 45 (21.9 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