Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate WP_159441877.1 BW971_RS15735 ABC transporter permease subunit
Query= TCDB::P48245 (273 letters) >NCBI__GCF_900156495.1:WP_159441877.1 Length = 460 Score = 97.8 bits (242), Expect = 4e-25 Identities = 70/225 (31%), Positives = 109/225 (48%), Gaps = 10/225 (4%) Query: 17 INSQTWTTY---ILPGLWGTLKSAV----FSVILALVMGTALGLGRISEIRILRWFCAVI 69 I TW +LP L TLK + S ++ LV+ + L R+S + F + Sbjct: 239 IAPSTWDVVGRNLLPMLGATLKGTIPLTAISFVVGLVIALVIALMRMSANPVASRFARLY 298 Query: 70 IETFRAIPVLILMIFAYQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLP 129 I R P+L+ + F + + IV + F + V ++ G AEI+RS I SLP Sbjct: 299 ISIIRGTPLLVQLFFIFFALPELGIVVNP---FPSAVVAFSLNVGGYAAEIIRSAIQSLP 355 Query: 130 KGQKEAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSG 189 KGQ EAA +GM R T ++LPQA +P L + ++ +KD++L I E+ R Sbjct: 356 KGQWEAASTIGMDYRTTLRRVILPQASRTAVPGLSNTLISLVKDTSLASGIQVAELFRKS 415 Query: 190 IQSASVNRNYLAALFVVALIMIVLNFSLTALASRIERQLRAGRAR 234 ++A+ +LA V A+I V+ L+ R+E +L AR Sbjct: 416 QEAAAPTFQFLALYGVAAVIYWVICLVLSFAQDRLETRLNRFVAR 460 Lambda K H 0.323 0.136 0.395 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: 300 Number of extensions: 10 Number of successful extensions: 3 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: 273 Length of database: 460 Length adjustment: 29 Effective length of query: 244 Effective length of database: 431 Effective search space: 105164 Effective search space used: 105164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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