Align Citrate:H+ symporter (characterized)
to candidate SMc01869 SMc01869 transport transmembrane protein
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Smeli:SMc01869 Length = 436 Score = 184 bits (468), Expect = 4e-51 Identities = 122/400 (30%), Positives = 195/400 (48%), Gaps = 10/400 (2%) Query: 36 GNFLEQFDFFLFGFYATYI-AHTFFPASSEFASLMMTFAVFGAGFLMRPIGAIVLGAYID 94 G +E FDF+++ A I H FFPA+ ++++ + A F F RP+GA++ G + D Sbjct: 33 GTTIEFFDFYVYATAAVIIFPHLFFPAADPTSAMLQSLATFSIAFFARPLGAVIFGHFGD 92 Query: 95 KVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAELGGVSVY 154 ++GR+ L+ L M T +I L+P+Y TIG+ APLL+ + R QG G E GG + Sbjct: 93 RIGRKATLVAALMTMGISTVVIGLLPTYSTIGVVAPLLLALCRFGQGLGLGGEWGGAVLL 152 Query: 155 LAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPFLFGVLIV 214 E A G++ +Y + + +++A L V+ A WGWR+PF+ VL+V Sbjct: 153 ATENAPEGKRSWYAMFPQLGAPIGFILSAGTFLILGEVMSEEAFLAWGWRVPFIASVLLV 212 Query: 215 PFIFILRRKLEETQEF--TARRHHLAMRQVFATLLANWQVVIAGMMMVAMTTTAFYLITV 272 +R K+ ET EF +H V A ++ + ++ G + T FYL+TV Sbjct: 213 IVGLYVRLKITETPEFQKAIDKHERVEVPVAAIFRSHKRSLVLGTFVALATFVLFYLMTV 272 Query: 273 YAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLIAMTLLALATAW 332 ++ ++G L S LLV + + +PV G LSDRFGRR VL+ T+ Sbjct: 273 FSLSWGTTKLGYSREQFLLVQMTGVVFFGLMIPVSGILSDRFGRRLVLVLTTIGIGVFGL 332 Query: 333 PALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLAYSLATAV 392 +L++ + S++ + G+ G + AL P VR G S+ ++LA Sbjct: 333 FMAPLLSSGLGGAFVFSIV--GLGLMGLTYGPIGAALAAPFPTAVRYTGASMTFNLAGIF 390 Query: 393 FGGFTPVISTALIEYTGDKASPGYWMSFAA----ICGLLA 428 P I+T L GY++ AA +C LL+ Sbjct: 391 GASLAPYIATWLAT-NYSLGHVGYYLLAAASITLVCLLLS 429 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: 528 Number of extensions: 47 Number of successful extensions: 4 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: 436 Length adjustment: 32 Effective length of query: 412 Effective length of database: 404 Effective search space: 166448 Effective search space used: 166448 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