Align Serine transporter (characterized)
to candidate 17600 b3539 predicted transporter (NCBI)
Query= SwissProt::Q8XAF5 (443 letters) >FitnessBrowser__Keio:17600 Length = 423 Score = 389 bits (1000), Expect = e-113 Identities = 188/416 (45%), Positives = 279/416 (67%), Gaps = 3/416 (0%) Query: 25 SEWREAIKFDSTDTGWVIMSIGMAIGAGIVFLPVQVGLMGLWVFLLSSVIGYPAMYLFQR 84 S+ + + F D GWV++ IGMAIGAG V +PVQ+GL G+WVF+ +++I YPA ++ Q Sbjct: 7 SKHNQKLPFTRYDFGWVLLCIGMAIGAGTVLMPVQIGLKGIWVFITAAIIAYPATWVVQD 66 Query: 85 LFINTLAESPECKDYPSVISGYLGKNWGILLGALYFVMLVIWMFVYSTAITNDSASYLHT 144 +++ TL+ES C DY +IS YLGKNWGI LG +YF+M++ +F+YS ++ DSASYL T Sbjct: 67 IYLKTLSESDSCNDYTDIISHYLGKNWGIFLGVIYFLMIIHGIFIYSLSVVFDSASYLKT 126 Query: 145 FGVTEGLLSDSPFYGLVLICILVAISSRGEKLLFKISTGMVLTKLLVVAALGVSMVGMWH 204 FG+T+ LS S Y + + +LVAI+S GE+LLFKIS MV+ K+ ++ G +M+ W+ Sbjct: 127 FGLTDADLSQSLLYKVAIFAVLVAIASGGERLLFKISGPMVVVKVGIIVVFGFAMIPHWN 186 Query: 205 LYNVGSLPPLGLLVKNAIITLPFTLTSILFIQTLSPMVISYRSREKSIEVARHKALRAMN 264 N+ + P + ++ ++T+PF S +FIQ L+PM I+YR RE +A ALR Sbjct: 187 FANITAFPQASVFFRDVLLTIPFCFFSAVFIQVLNPMNIAYRKREADKVLATRLALRTHR 246 Query: 265 IAFGILFIIVFFYAVSFTLAMGHDEAVKAYEQNISALAIAAQFISGDGAAWVKVVSVILN 324 I++ L ++ F+A SFT ++ H+EAV A+EQNISALA+AAQ I G + + S +LN Sbjct: 247 ISYITLIAVILFFAFSFTFSISHEEAVSAFEQNISALALAAQVIPGH---IIHITSTVLN 303 Query: 325 IFAVMTAFFGVYLGFREATQGIVMNILRRKMPAEKINENLVQRGIMIFAILLAWSAIVLN 384 IFAV+TAFFG+YLGF EA +GI++N+L R + +KIN ++ I F ++ + Sbjct: 304 IFAVLTAFFGIYLGFHEAIKGIILNLLSRIIDTKKINSRVLTLAICAFIVITLTIWVSFR 363 Query: 385 APVLSFTSICSPIFGLVGCLIPAWLVYKVPALHKYKGMSLYLIIVTGLLLCVSPFL 440 VL F + SP++G+V CLIP +L+YKV L K +G +LI++ G+LLC+SP L Sbjct: 364 VSVLVFFQLGSPLYGIVSCLIPFFLIYKVAQLEKLRGFKAWLILLYGILLCLSPLL 419 Lambda K H 0.328 0.141 0.424 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: 570 Number of extensions: 30 Number of successful extensions: 2 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: 443 Length of database: 423 Length adjustment: 32 Effective length of query: 411 Effective length of database: 391 Effective search space: 160701 Effective search space used: 160701 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 (21.7 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