Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate SMa2197 SMa2197 ABC transporter permease
Query= TCDB::P48245 (273 letters) >FitnessBrowser__Smeli:SMa2197 Length = 304 Score = 97.8 bits (242), Expect = 2e-25 Identities = 69/226 (30%), Positives = 116/226 (51%), Gaps = 18/226 (7%) Query: 30 LWG---TLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFAY 86 LWG T+ V ++++ +V+GT + +++ ++ I FR PVL+ +IF Y Sbjct: 67 LWGLSLTVWLTVVTMVIGVVLGTIFAIMAMADNVVISTVANAYIWFFRGTPVLVQLIFWY 126 Query: 87 QM---FAQYNI----------VPSSQLA--FAAVVFGLTMYNGSVIAEILRSGIASLPKG 131 + F Q ++ VP++ L A V GL + G+ ++EI+RSG+ S+ G Sbjct: 127 NLGALFPQLSVGVPFTSLWVSVPTNTLISPVTAAVLGLGLNEGAYMSEIIRSGLMSVDPG 186 Query: 132 QKEAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQ 191 Q++AA +LGM++ +T W ILLPQA+ ++P +Q + LK S+L I +++ S Sbjct: 187 QRQAAKSLGMTNGKTLWRILLPQAMPVIIPPTGNQTIGMLKTSSLVSVISLADLLYSAQT 246 Query: 192 SASVNRNYLAALFVVALIMIVLNFSLTALASRIERQLRAGRARKNI 237 S N + L V + + L+A+ RIER R NI Sbjct: 247 IYSRNFQTIPLLIVACIWYLAATTILSAVQVRIERHFARSSQRANI 292 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: 194 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 273 Length of database: 304 Length adjustment: 26 Effective length of query: 247 Effective length of database: 278 Effective search space: 68666 Effective search space used: 68666 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: 47 (22.7 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