Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate 8502448 DvMF_3154 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::P48245 (273 letters) >FitnessBrowser__Miya:8502448 Length = 229 Score = 112 bits (281), Expect = 5e-30 Identities = 75/225 (33%), Positives = 123/225 (54%), Gaps = 22/225 (9%) Query: 25 YILPGLW--GTLKSAVFSVILALV-------MGTALGLGRISEIRILRWFCAVIIETFRA 75 Y+L G W G L SV+LA+ +G GL R+S+ LR + +E R Sbjct: 12 YLLVGSWPQGPLGGLAMSVVLAIGGIFGAFWLGLGFGLLRLSDRWWLRLPAIIYVEIIRG 71 Query: 76 IPVLILMIFAYQM--FAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQK 133 IP+L+L+ + Y + +P ++ A A + ++ G+ IAEI+R+G+ +LP GQ Sbjct: 72 IPLLMLIFWFYFLAPIVLGRTLPEAESALVAFI----VFTGAYIAEIVRAGVLALPHGQM 127 Query: 134 EAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSA 193 EAA G+S Q ++LPQA+ M+P+ ++Q V KD++L Y IG E+ R+ Q Sbjct: 128 EAARGTGLSKSQAMIYVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSELTRTATQ-- 185 Query: 194 SVNRNYLAA----LFVVALIMIVLNFSLTALASRIERQLRAGRAR 234 +N L A F +A++ ++ ++LTA + R+ERQ+ +AR Sbjct: 186 -INNRELTAPAELFFTIAVLYFIVCWTLTAASRRMERQMARYQAR 229 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: 170 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 273 Length of database: 229 Length adjustment: 24 Effective length of query: 249 Effective length of database: 205 Effective search space: 51045 Effective search space used: 51045 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: 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