Align neutral amino acid transporter A (characterized)
to candidate Echvi_1519 Echvi_1519 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__Cola:Echvi_1519 Length = 444 Score = 213 bits (541), Expect = 2e-59 Identities = 148/430 (34%), Positives = 234/430 (54%), Gaps = 39/430 (9%) Query: 52 VLAGAGLGAALRGLSLSRTQVT------YLAFPGEMLLRMLRMIILPLVVCSLVSGAASL 105 ++ G LG GL + +TQ++ Y+ G + + L+MI +PLV+ SL+ G ++L Sbjct: 11 IIIGLVLGLVF-GLIVIKTQMSPDFTMDYIKPIGTIFINGLKMIAVPLVLASLIVGVSNL 69 Query: 106 -DASCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVP 164 D + LGR+GG + + +TT+ A + + L + PG +P Sbjct: 70 GDITKLGRIGGKTIGAYMMTTVIAVTVGLLLVNVFAPGKS------------------LP 111 Query: 165 KETVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNIL 224 ET + ++ + VV + A + K T ++ E + + G ++L Sbjct: 112 IETRERLMEQFDD------VVGDKSSQAAELKEQTPLKPLVDMVPENVFLAAADNG-SML 164 Query: 225 GLVLFALVLGVALKKLG-SEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVE 283 +V FA+++G+AL ++ S+ +I FF+ LN+ + +V +IM P G+ L+ S IVE Sbjct: 165 QVVFFAIIVGIALLEIPKSKASPVIAFFDGLNDVIIKIVGYIMLIAPYGVFALMASLIVE 224 Query: 284 MK-----DIIVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFAT 338 + I L+ +L KY + G ++ +V P I +FT+ F L Sbjct: 225 IAGDNPDSAIELLFALLKYSLLVVAGLLLMIVLVYPTILKLFTKVKYKDFFAALRPAQLL 284 Query: 339 AFATCSSSATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNN 398 AF+T SSSATLP MK +EE GV + +S F+LP+GAT+NMDG ++Q VAAVFIAQ Sbjct: 285 AFSTSSSSATLPVTMKQVEEEIGVSEEVSSFVLPLGATINMDGTCLYQGVAAVFIAQALG 344 Query: 399 VELNAGQIFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRT 458 ++L+ Q I++TAT +S+G AGVP G++ + I+LE+IG+P+ L LILA D I+D Sbjct: 345 LDLSLTQQLMIVLTATLASIGTAGVPGAGLIMLLIVLESIGVPSAGLALILAPDRILDMF 404 Query: 459 TTVVNVEGDA 468 TVVNV GDA Sbjct: 405 RTVVNVTGDA 414 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: 405 Number of extensions: 14 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: 532 Length of database: 444 Length adjustment: 34 Effective length of query: 498 Effective length of database: 410 Effective search space: 204180 Effective search space used: 204180 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