Align neutral amino acid transporter A (characterized)
to candidate GFF4002 Psest_4075 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__psRCH2:GFF4002 Length = 419 Score = 210 bits (534), Expect = 9e-59 Identities = 144/436 (33%), Positives = 225/436 (51%), Gaps = 58/436 (13%) Query: 52 VLAGAGLGAALRGLSLSRTQVTYLAFPGEMLLRMLRMIILPLVVCSLVSGAASL-DASCL 110 +L G LG A G++ LA G + L ++M+I+PLV SLV+G S+ D++ L Sbjct: 23 ILIGLALGVAA-GMAFG-ADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSAKL 80 Query: 111 GRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKETVDS 170 GR+ +A + +TT A ++ + + PG G + S G E + P S Sbjct: 81 GRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVAS---GNEQAKQAP-------S 130 Query: 171 FLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLVLFA 230 + + L P+N P+ EG NIL +++FA Sbjct: 131 LVSILVGLVPAN------------------------------PVTAFAEG-NILQIIVFA 159 Query: 231 LVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFL----VGSKIVEMKD 286 + LGV++ +G G +R F++L E L +M P+G+ L VGS E+ Sbjct: 160 IALGVSINLIGERGAPAVRLFDALAETFYKLTDLVMRVAPIGVFALTAGVVGSHGAEV-- 217 Query: 287 IIVLVTSLGKYIFASILGHV--IHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATCS 344 ++ L +G ASI HV ++GG++ + R NP RF G+ A AF+T S Sbjct: 218 LLPLAGVIGVIYLASI-AHVLLVYGGLL-----GLLARLNPLRFFQGIAPALAVAFSTSS 271 Query: 345 SSATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNAG 404 SS TLP ++C +N GV + ++ F+LP+GAT+NMDG AI+Q V A+FIAQ ++L+AG Sbjct: 272 SSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGVLALFIAQAFGIDLSAG 331 Query: 405 QIFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVNV 464 Q I++TAT +S+G AG+P G++ + ++L A GLP + LI +D I+D T VNV Sbjct: 332 QYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALIAGIDRILDMARTTVNV 391 Query: 465 EGDALGAGILHHLNQK 480 GD + ++ Q+ Sbjct: 392 AGDLMTTTLVGRSEQE 407 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: 395 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 532 Length of database: 419 Length adjustment: 33 Effective length of query: 499 Effective length of database: 386 Effective search space: 192614 Effective search space used: 192614 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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