Align Citrate:H+ symporter (characterized)
to candidate GFF4424 PS417_22650 MFS transporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__WCS417:GFF4424 Length = 439 Score = 238 bits (608), Expect = 2e-67 Identities = 136/391 (34%), Positives = 205/391 (52%), Gaps = 4/391 (1%) Query: 11 SSTAPVRMMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMM 70 S+ AP + T+ +RI +I + GN +E +D++++ ++ Y A FFP A L+ Sbjct: 11 SAAAPAKARTTS--SRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLN 68 Query: 71 TFAVFGAGFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAP 130 T A+F GFLMRPIG ++G Y DKVGR+K L+ ++ +M G+ LI L P Y+ IG+ AP Sbjct: 69 TAAIFAVGFLMRPIGGWLMGLYADKVGRKKALMASVYLMCFGSLLIALSPGYEIIGIGAP 128 Query: 131 LLVLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALN 190 +L++ RLLQG S G E G + YL+E+AT R+GFY+S+Q + ++A A+ L Sbjct: 129 ILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFYSSFQYVTLISGQLIALAVLIVLQ 188 Query: 191 AVLEPSAISDWGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLANW 250 VL + WGWRIPF G L LRR +EET+ FT + A TL+ + Sbjct: 189 QVLTTEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKEK--AKESAMRTLMRHP 246 Query: 251 QVVIAGMMMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGAL 310 + ++ + + T AFY T Y + + +S SDS ++ P+ G L Sbjct: 247 KELLTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIVGGL 306 Query: 311 SDRFGRRSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALT 370 SD+ GRR +LIA +L P LT L S+ +++ I Y Sbjct: 307 SDKVGRRPILIAFGILGTLFTVPILTTLHTIQSWWGAFFLIMAALIIVSGYTSINAVVKA 366 Query: 371 EIMPAEVRVAGFSLAYSLATAVFGGFTPVIS 401 E+ P E+R G L Y+L ++FGG I+ Sbjct: 367 ELFPTEIRALGVGLPYALTVSIFGGTAEYIA 397 Lambda K H 0.329 0.139 0.421 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: 486 Number of extensions: 25 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: 444 Length of database: 439 Length adjustment: 32 Effective length of query: 412 Effective length of database: 407 Effective search space: 167684 Effective search space used: 167684 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 51 (24.3 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