Align Citrate:H+ symporter (characterized)
to candidate GFF1547 Psest_1584 Arabinose efflux permease
Query= TCDB::P16482 (444 letters) >FitnessBrowser__psRCH2:GFF1547 Length = 452 Score = 290 bits (742), Expect = 6e-83 Identities = 156/420 (37%), Positives = 233/420 (55%), Gaps = 1/420 (0%) Query: 18 MMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGA 77 M + R +L GN LE +DF +FGF A I+ FFPA SE+++L+M A FG Sbjct: 1 MSNSTAAPRKNQVLAAVIGNALEWYDFIVFGFLAVVISRLFFPAESEYSALLMATATFGV 60 Query: 78 GFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGR 137 GF MRPIG ++LG Y D+ GR+ L + +S+M +I P + IG+ APLL+++ R Sbjct: 61 GFFMRPIGGVLLGIYADRKGRKAALQLIISLMTLSIAMIAFAPPFAAIGIAAPLLIVLAR 120 Query: 138 LLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSA 197 L+QGF+ G E + +L E A R+G Y SWQ Q +A+ A + + + L P Sbjct: 121 LMQGFATGGEFASATSFLIESAPANRRGLYGSWQMFGQGLAVFCGAGVTALVTSNLSPED 180 Query: 198 ISDWGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLL-ANWQVVIAG 256 + WGWRIPF+ G++I P +RR L ET+ F R +Q A +L ++ + V+ Sbjct: 181 LDSWGWRIPFIIGLIIGPVGLWMRRNLSETEAFLEARQAPKEKQSLARMLRSHLRQVVTV 240 Query: 257 MMMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGR 316 M + T AFY+I VY PTF + L + D+ ++ +PV GALSDR GR Sbjct: 241 MALTVCGTVAFYVILVYMPTFANRQLGMQLKDAFTAQVVAVAVLTLLMPVFGALSDRVGR 300 Query: 317 RSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAE 376 + ++I TL L +P + + APSF +L++ L L + ++ G A+ E PA Sbjct: 301 KLLMIVATLGLLVALYPLFSWIHAAPSFGRLLTMQLILCSLLAVFFGPFSAAVAEQFPAG 360 Query: 377 VRVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLATCYLYRRS 436 VR G +LAY+LA +FGGF I T LI+ TG +P +++ FA GL+ + +L R+ Sbjct: 361 VRSTGLALAYNLAVMIFGGFAQFIVTWLIQNTGMAIAPVFYVLFAVTLGLIGSFFLIDRT 420 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: 552 Number of extensions: 26 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: 452 Length adjustment: 33 Effective length of query: 411 Effective length of database: 419 Effective search space: 172209 Effective search space used: 172209 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