Align Citrate:H+ symporter (characterized)
to candidate H281DRAFT_04666 H281DRAFT_04666 MFS transporter, MHS family, proline/betaine transporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Burk376:H281DRAFT_04666 Length = 425 Score = 310 bits (795), Expect = 4e-89 Identities = 161/401 (40%), Positives = 242/401 (60%), Gaps = 6/401 (1%) Query: 29 AILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMRPIGAIV 88 A++ + GN LE FD ++GF+A IA FFPA ++ SL++T FG F MRP+GAIV Sbjct: 19 AVIAASIGNALEWFDLVVYGFFAVVIAKLFFPAGNDTVSLLLTLGTFGVSFFMRPLGAIV 78 Query: 89 LGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAEL 148 +GAY D+ GR+ L +++ +M GT +I ++P+Y++IG+ AP++++I RL+QGFSAG E Sbjct: 79 IGAYADRAGRKAALTLSILLMMGGTLIIAVLPTYRSIGIAAPVILVIARLMQGFSAGGEF 138 Query: 149 GGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPFL 208 G + +LAE PGR+GF+ SWQ SQ + ++AA G AL L P ++ WGWR+PF Sbjct: 139 GSATAFLAE-HVPGRRGFFASWQVASQGLTTLLAAGFGVALTGNLTPDQMASWGWRVPFF 197 Query: 209 FGVLIVPFIFILRRKLEETQEF-TARRHHLAMRQVFATLLANWQVVIAGMMMVAMTTTAF 267 FG+LI P + +R KL+ET EF A +R F + + I V + T + Sbjct: 198 FGLLIGPVAWYIRTKLDETPEFLAAETTSTPLRDTFTSQKLRLLIAIGA---VVLGTVST 254 Query: 268 YLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLIAMTLLA 327 YL+ ++ PTFG K L L+ S + L + + PV G LSDR GR ++++ +L Sbjct: 255 YLV-LFMPTFGVKQLGLAPSVAFSAIALTGLIQMVFAPVVGHLSDRHGRTTIMLISAVLL 313 Query: 328 LATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLAYS 387 L +PA L P+F ++++ + L F+ Y A+ L+E+ P + R G SLAY+ Sbjct: 314 LVLIYPAFVYLVAHPTFGTLIALQVVLGFLMTGYFAALPGLLSEMFPVQTRTTGMSLAYN 373 Query: 388 LATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLA 428 +A VFGGF P I LI +TG KA+P Y++ FAA+ + A Sbjct: 374 IAVTVFGGFGPFIIAWLIGFTGSKAAPSYYLIFAALLSVAA 414 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: 580 Number of extensions: 33 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 412 Effective length of database: 393 Effective search space: 161916 Effective search space used: 161916 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