Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate HSERO_RS11450 HSERO_RS11450 ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >FitnessBrowser__HerbieS:HSERO_RS11450 Length = 257 Score = 264 bits (674), Expect = 1e-75 Identities = 137/246 (55%), Positives = 180/246 (73%), Gaps = 5/246 (2%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 +++++G++K FG L D+DL + QVVVV+GPSGSGKST R +N LE E GT+++ Sbjct: 5 IVEVSGLRKSFGAHVVLKDLDLSVAPSQVVVVIGPSGSGKSTFLRCLNGLEKAEGGTVKV 64 Query: 61 DGKVLPEEGKGLAN-----LRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEK 115 G+ + E G+ + LRA+VGMVFQSFNLFPHLT+ DN+TLAP +R M + A++ Sbjct: 65 CGRPVVEGGRMMPEAMLDLLRAEVGMVFQSFNLFPHLTVLDNITLAPTCLRGMSRKAAQQ 124 Query: 116 LAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEV 175 A+ LLE+VG+A++A YP LSGGQ+QRVAIARALAM P++MLFDEPTSALDPE+V EV Sbjct: 125 QALQLLEKVGLAHKAKAYPGTLSGGQKQRVAIARALAMEPQVMLFDEPTSALDPELVGEV 184 Query: 176 LDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDF 235 L V+ +LA EGMTM+ VTHEMGFAR+ AD V+ M G IVE P + FT P+ R + F Sbjct: 185 LQVIRALAAEGMTMIIVTHEMGFAREVADVVVVMDHGSIVEAGPPGAIFTAPQQARTRSF 244 Query: 236 LGKILA 241 L +LA Sbjct: 245 LQTMLA 250 Lambda K H 0.319 0.135 0.379 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: 201 Number of extensions: 4 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: 242 Length of database: 257 Length adjustment: 24 Effective length of query: 218 Effective length of database: 233 Effective search space: 50794 Effective search space used: 50794 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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