Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate WP_057508795.1 ABB28_RS11690 dicarboxylate/amino acid:cation symporter
Query= uniprot:L0GT47 (419 letters) >NCBI__GCF_001431535.1:WP_057508795.1 Length = 443 Score = 303 bits (776), Expect = 7e-87 Identities = 164/421 (38%), Positives = 252/421 (59%), Gaps = 21/421 (4%) Query: 15 VRLPLWQQILIGLALGVAAGMAFGADAQL-LAPIGTLFLNAIKMLIVPLVFVSLVAGITS 73 +R+P WQ+++ G LG AG G A+ P+G L++ IKM+ VPLVF +++ I+S Sbjct: 8 LRIPFWQRVVAGFVLGALAGWLMGPAAETWFGPLGDLYVTLIKMIAVPLVFFAVINAISS 67 Query: 74 MQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEG-MNMVASGNEQAKQAPSLV 132 + + +S +T +++T A AV IGLL G + PG G + + + N ++ PS+V Sbjct: 68 LHGQKSVAALSGRTFLWFVITAALAVGIGLLVGTVMQPGTGGLQLAMAHNYVPREVPSVV 127 Query: 133 SILVGLVPAN-----------------PVTAFAEGNILQIIVFAIALGVSINLIGERGAP 175 +L+ +VP+N V A G+IL +I FA +G +I +GE+ Sbjct: 128 QVLLDVVPSNVFYALSGIGTRVNAAGETVLAAGRGSILPVIFFAGLVGFAIVKLGEKVGQ 187 Query: 176 AVRLFDALAETFYKLTDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAH 235 A +L ++E ++T V+ V PIG F L AG+VGS+G E LLPL + +Y+A H Sbjct: 188 ARQLVGQMSEIMIQVTRFVLEVTPIGTFGLIAGLVGSYGFEKLLPLGNFVLALYIACALH 247 Query: 236 VLLVYGGLLGLLARLNPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAG 295 +++VY LL L LNPL+FF+G AP + VAF +SSS +PV++ NLGV++ Sbjct: 248 IVVVYSALL-LSHGLNPLKFFRGAAPGMQVAFVSSSSFAAMPVALRSITHNLGVNKDYGS 306 Query: 296 FVLPVGATINMDGT-AIYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAG 354 F +P+GA+I MDG AIY + A+FI+Q G+ +S QY ++++ + L S GTAG+PG Sbjct: 307 FAVPLGASIKMDGCGAIYPALCAVFISQYSGVPMSPEQYLIVLIASVLGSFGTAGVPGTA 366 Query: 355 LIMLGLVLTAAGLPLEGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYD 414 ++M +VL+AAGLPLE + + IDRILDM RT NV G ++ LV + LD+++YD Sbjct: 367 VVMATVVLSAAGLPLETIGYLYAIDRILDMMRTMTNVTGQMLVPVLVAKETGLLDQSVYD 426 Query: 415 S 415 + Sbjct: 427 N 427 Lambda K H 0.324 0.140 0.386 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: 546 Number of extensions: 29 Number of successful extensions: 6 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: 419 Length of database: 443 Length adjustment: 32 Effective length of query: 387 Effective length of database: 411 Effective search space: 159057 Effective search space used: 159057 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: 41 (22.0 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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