Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate YP_004141778.1 Mesci_2592 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::P48244 (228 letters) >NCBI__GCF_000185905.1:YP_004141778.1 Length = 244 Score = 100 bits (250), Expect = 2e-26 Identities = 70/206 (33%), Positives = 102/206 (49%), Gaps = 11/206 (5%) Query: 10 PSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVL 69 P LL WVT LT S + G L MR+S + L + Y N R TPL + + Sbjct: 10 PVLLKGLWVTAALTFVSVLIGFNLGLGLALMRLSSNRFLSGFAKYYSNVFRGTPLLVQIF 69 Query: 70 FCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAE 129 +GL Q ++ + +L+ + R AVL L T+ + +E LR G+ +V G E Sbjct: 70 LFYYGLGQLS--SIKDNAALWWLISDGARCAVLALALNTAAYTSEILRGGLMSVPVGLVE 127 Query: 130 AARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGV----GEASLLMK 185 AA++ G+ FR I FP A+R A+ GN LI + K T++AS I V G A LM Sbjct: 128 AAQACGMSRMLRFRRIEFPLAIRQALPAYGNELILVVKGTSLASTITVLEITGYAKRLMS 187 Query: 186 ATIENHANMLFVVFAIFAVGFMILTL 211 T +F +FAI V ++++ L Sbjct: 188 QTF-----AIFEIFAIAGVLYLVINL 208 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: 132 Number of extensions: 7 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: 244 Length adjustment: 23 Effective length of query: 205 Effective length of database: 221 Effective search space: 45305 Effective search space used: 45305 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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