Align Possible transporter of polar amino acids including glutamate, glutamine and aspartate, DmeA. It complements a sepJ mutation in Anabaena (TC# 2.A.7.23.2), and SepJ complements a dmeA mutation. Alternatively, and less likely, it could be an activator of an ABC transporter catalyzing uptake of these amino acids (characterized)
to candidate RR42_RS28180 RR42_RS28180 membrane protein
Query= TCDB::Q31PG5 (330 letters) >FitnessBrowser__Cup4G11:RR42_RS28180 Length = 298 Score = 96.3 bits (238), Expect = 9e-25 Identities = 90/292 (30%), Positives = 134/292 (45%), Gaps = 22/292 (7%) Query: 20 VSLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPPLNRRQ 79 +S+ L++A ALWG ++ R+ + + +A R A +LL +L R G L RR Sbjct: 6 LSMLLSLA-ALWGASYLFIRLGAGEFGAVPLAGARAGGAALLLLPLLAWRGGLACLRRRW 64 Query: 80 QLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWA 139 + +G++ AL LF IPA +A+ A P AL +W + L + + A Sbjct: 65 WAIAV-VGITNSALPFVLFSFAALTIPAGLSAMFTAATPLFTALIGWLWLRENLEAPRIA 123 Query: 140 GVGLSLIGAILLL----GSRQAGALTLPGWGDLALVGCVLCWTVYSLLARQALRSLSPLT 195 G+ L G + L+ G +Q A G LA + L + + R+ L + PLT Sbjct: 124 GLALGFAGVLWLVWDKAGLQQGAAGKAAGLAALACLAAALLYGFSANFTRKYLADVPPLT 183 Query: 196 VTTGACCWGSVLLIG--LWLGQGAQLPVNVSFSTGSAIAFLGLGG-----TALAFCLYAN 248 V G+ ++LL WL Q SA A+L LG TALA+ L+ Sbjct: 184 VAAGSQLASALLLCAPAAWLWPATQ---------PSAHAWLALGALTAACTALAYVLFFR 234 Query: 249 GIERLGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGLGT 300 I + G ARA + L+P FG GAL L E ++ L G ++LAG L T Sbjct: 235 LIAKAGPARAMTALFLIPAFGVLWGALFLGERITPSMLPGCAVILAGTALTT 286 Score = 33.1 bits (74), Expect = 9e-06 Identities = 37/135 (27%), Positives = 54/135 (40%), Gaps = 4/135 (2%) Query: 21 SLQLAIATALWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLILWQREGWPPL--NRR 78 +L A L+G + R + + PL VA G L + LLL WP + Sbjct: 155 ALACLAAALLYGFSANFTRKYLADVPPLTVAAGSQL--ASALLLCAPAAWLWPATQPSAH 212 Query: 79 QQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQW 138 L L L + AL LFF ++ +RA + L P L A++ G+R+ Sbjct: 213 AWLALGALTAACTALAYVLFFRLIAKAGPARAMTALFLIPAFGVLWGALFLGERITPSML 272 Query: 139 AGVGLSLIGAILLLG 153 G + L G L G Sbjct: 273 PGCAVILAGTALTTG 287 Lambda K H 0.325 0.142 0.454 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: 335 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 330 Length of database: 298 Length adjustment: 27 Effective length of query: 303 Effective length of database: 271 Effective search space: 82113 Effective search space used: 82113 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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