Align neutral amino acid transporter B(0) (characterized)
to candidate 6936881 Sama_1055 sodium:dicarboxylate symporter (RefSeq)
Query= CharProtDB::CH_091706 (553 letters) >FitnessBrowser__SB2B:6936881 Length = 417 Score = 176 bits (447), Expect = 1e-48 Identities = 135/463 (29%), Positives = 218/463 (47%), Gaps = 69/463 (14%) Query: 61 VVAGVGLGL--GVSAAGGADALGPARLTRFAFPGELLLRLLKMIILPLVVCSLIGGAASL 118 V+AG LG+ GV A L P G+L + +KM++ PLV+C+++ SL Sbjct: 15 VLAGFALGILTGVLLGESATVLKPL--------GDLFIAAIKMLVAPLVLCAIVVSITSL 66 Query: 119 DPSA-LGRVGAWALLFFLVTTLLASALGVGLALALKPGAAVT-AITSINDSVVDPCARSA 176 S+ L R+ L F++T LAS +G+ + + G ++ A T + + VV Sbjct: 67 GSSSNLKRLSFKTLALFMLTGTLASLIGLAVGSSFDMGGSMQLASTEVRERVVP------ 120 Query: 177 PTKEALDSFLDLVRNIFPSNLVSAAFRSFATSYEPKDNSCKIPQSCIQREINSTMVQLLC 236 F ++ ++ P N FA+ K Sbjct: 121 -------GFAQVLLDMIPVN-------PFASLTNGK------------------------ 142 Query: 237 EVEGMNILGLVVFAIVFGVALRKLGPEGELLIRFFNSFNDATMVLVSWIMWYAPVGILFL 296 +L ++VFA + G+A+ +G + E L + F++ + L ++ P+G+ L Sbjct: 143 ------VLQIIVFAALVGIAINAVGEKAEPLKKVFDAGAEVMFQLTRMVLKLTPIGVFGL 196 Query: 297 VASKIVEMKDVRQLFISLGKYILCCLLGHAIHGLLVLPLIYFLFTRKNPYRFLWGIMTPL 356 +A + E + LGK+I+ + IH + V + R +P +F M Sbjct: 197 MAWVVGEYG--LSTLLPLGKFIIAIYVAALIHIVFVYGGLVKFAARLSPLQFFRKAMPAQ 254 Query: 357 ATAFGTSSSSATLPLMMKCVEEKNGVAKHISRFILPIGATVNMDGAA-LFQCVAAVFIAQ 415 AF T+SS TLP+ KC E GV+K S F+LP+GAT+NMDG ++ +AA+FIAQ Sbjct: 255 LVAFSTASSFGTLPVTTKCAESM-GVSKRYSAFVLPMGATMNMDGCGGIYPAIAAIFIAQ 313 Query: 416 LNGVSLDFVKIITILVTATASSVGAAGIPAGGVLTLAIILEAVSLPVKDISLILAVDWLV 475 + G+ LD + I VTAT +SVG AG+P ++ L + L V LP++ I+ I A+D ++ Sbjct: 314 IYGIPLDMTDYMLIAVTATVASVGTAGVPGSAMVMLTVTLGVVGLPLEGIAFIAAIDRVI 373 Query: 476 DRSCTVLNVEGDAFGA---GLLQSYVDRTKMPSSEPELIQVKN 515 D T NV GD A G + +DR + +E + I N Sbjct: 374 DMIRTCTNVTGDMMTAVVVGNSEGELDRERFYKAEEDKIVADN 416 Lambda K H 0.323 0.138 0.406 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: 447 Number of extensions: 22 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: 553 Length of database: 417 Length adjustment: 34 Effective length of query: 519 Effective length of database: 383 Effective search space: 198777 Effective search space used: 198777 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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