Align neutral amino acid transporter A (characterized)
to candidate 201109 SO1948 sodium:dicarboxylate symporter family protein (NCBI ptt file)
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__MR1:201109 Length = 437 Score = 207 bits (527), Expect = 6e-58 Identities = 136/402 (33%), Positives = 209/402 (51%), Gaps = 44/402 (10%) Query: 74 YLAFPGEMLLRMLRMIILPLVVCSLVSGAASL-DASCLGRLGGIAVAYFGLTTLSASALA 132 +L G + + L+M+++PLV SLV G SL + S LGRLGG +A++ TT+ A LA Sbjct: 47 FLHVIGTIFISSLKMLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTVLALVLA 106 Query: 133 VALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKETVDSFLDLARNLFPSNLVVAAFRTYA 192 V A I+ PG TL + L V KE SF + ++ P+N Sbjct: 107 VFAAVIVHPGDA--TLANEKLNY-------VAKE-APSFAQVIIDMMPTN---------- 146 Query: 193 TDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLVLFALVLGVALKKLGSEGEDLIRFFN 252 P+ EG N+L +++FA++ G A+ LG G + + F+ Sbjct: 147 --------------------PVQAMSEG-NMLQIIIFAVIFGFAIAHLGERGNRIAQLFD 185 Query: 253 SLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMKDIIVLVTSLGKYIFASILGHVIHGGIV 312 LN M +V+ +M P G+ L+ + + + S+ KY F + +IH + Sbjct: 186 DLNNVIMRVVTLVMQLAPYGVFALMAKLALTLG--LETFGSVVKYFFLVLTLLLIHNFVT 243 Query: 313 LPLIYFVFTRKNPFRFLLGLLAPFATAFATCSSSATLPSMMKCIEENNGVDKRISRFILP 372 ++ F+ NP F+ + AF+T SS+ATLP ++ E GVD +I+ F LP Sbjct: 244 YSILLKAFSGLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASFTLP 303 Query: 373 IGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQIFTILVTATASSVGAAGVPAGGVLTIA 432 +GAT+NMDG AI Q VA VFIAQ+ +EL+ ++VTAT +S+G AGVP G++ +A Sbjct: 304 LGATINMDGTAIMQGVATVFIAQVFGIELSLTDYAAVIVTATLASIGTAGVPGVGLIMLA 363 Query: 433 IILEAIGLPTHDLPLILAVDWIVDRTTTVVNVEGDALGAGIL 474 ++L +GLP + LI+ VD ++D T VNV GD + I+ Sbjct: 364 MVLNQVGLPVEGIALIIGVDRLLDMVRTAVNVTGDCVATVII 405 Lambda K H 0.320 0.136 0.390 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: 347 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 532 Length of database: 437 Length adjustment: 34 Effective length of query: 498 Effective length of database: 403 Effective search space: 200694 Effective search space used: 200694 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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