Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate GFF4002 Psest_4075 Na+/H+-dicarboxylate symporters
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__psRCH2:GFF4002 Length = 419 Score = 354 bits (909), Expect = e-102 Identities = 188/411 (45%), Positives = 264/411 (64%), Gaps = 12/411 (2%) Query: 8 KIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLV 67 ++ L +ILIG+ G+ G+ FG + IGT+F+N++KML+VPLV Sbjct: 16 RLPLWQQILIGLALGVAAGMA----FGADAQL--------LAPIGTLFLNAIKMLIVPLV 63 Query: 68 FISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQY 127 F+SLV G S+ + +KLGR+ KT+A YL TTA A+ + + L PG S Sbjct: 64 FVSLVAGITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNE 123 Query: 128 SAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDL 187 AK+APSL +L+ +VP+NP+ A +EGN+LQII+FA+ G +I+ IGERG LFD L Sbjct: 124 QAKQAPSLVSILVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDAL 183 Query: 188 NEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTL 247 E ++ L+M++AP GVFAL + + G E L + ++ + + H +VY L Sbjct: 184 AETFYKLTDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGL 243 Query: 248 LKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGAT 307 L L + L+PL F + + AFST+SS+ TLPV++E + LG VA F LP+GAT Sbjct: 244 LGLLARLNPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGAT 303 Query: 308 INMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLN 367 INMDGTAI QGV +FIAQ FGIDL+ YAM+++TATLASIGTAG+PG GL+ML +VL Sbjct: 304 INMDGTAIYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLT 363 Query: 368 QVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFN 418 GLP+EG+ALI G+DR+LDM RT VNV GD + T ++ +SE L+ A+++ Sbjct: 364 AAGLPLEGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYD 414 Lambda K H 0.325 0.139 0.388 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: 448 Number of extensions: 15 Number of successful extensions: 1 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: 437 Length of database: 419 Length adjustment: 32 Effective length of query: 405 Effective length of database: 387 Effective search space: 156735 Effective search space used: 156735 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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