Align neutral amino acid transporter A (characterized)
to candidate 7024548 Shewana3_1726 sodium:dicarboxylate symporter (RefSeq)
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__ANA3:7024548 Length = 437 Score = 212 bits (539), Expect = 3e-59 Identities = 148/478 (30%), Positives = 233/478 (48%), Gaps = 75/478 (15%) Query: 51 GVLAGAGLGAALRGL----SLSRTQVT--YLAFPGEMLLRMLRMIILPLVVCSLVSGAAS 104 G+ G LG LR + + + +T +L G + + L+M+++PLV SLV G S Sbjct: 18 GMATGIALGLILRNVFPESDIVKDYITEGFLHVIGTIFISSLKMLVVPLVFISLVCGTCS 77 Query: 105 L-DASCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPV 163 L + S LGRLGG +A++ TT A LA+ A ++ PG+ + + + +++ Sbjct: 78 LSEPSKLGRLGGKTLAFYLFTTAIALILAIVSAVLVHPGNASLASEKMEYTAKEA----- 132 Query: 164 PKETVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNI 223 S + N+ P+N P+ EG N+ Sbjct: 133 -----PSLSSVLINIVPTN------------------------------PMQAMSEG-NM 156 Query: 224 LGLVLFALVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVE 283 L +++FA++ G A+ +G G+ + F LNE M +V+ IM P G+ L+ + Sbjct: 157 LQIIIFAVIFGFAIAHIGERGKRVAALFEDLNEVIMRVVTLIMQLAPYGVFALMAKLALT 216 Query: 284 MKDIIVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATC 343 + + S+ KY F ++ +IH IV P + +F+ NP F+ + AF+T Sbjct: 217 LG--LGTFESVVKYFFVVLVVLLIHAFIVYPTLLKLFSGLNPLIFIRKMRDVQLFAFSTA 274 Query: 344 SSSATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNA 403 SS+ATLP ++ E GVD +I+ F LP+GAT+NMDG AI Q VA VFIAQ+ +EL Sbjct: 275 SSNATLPITIEASEHRLGVDNKIASFTLPLGATINMDGTAIMQGVATVFIAQVFGIELTI 334 Query: 404 GQIFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVN 463 ++VTAT +S+G AGVP G++ +A++L +GLP + LI+ VD ++D T VN Sbjct: 335 TDYAAVVVTATLASIGTAGVPGVGLIMLAMVLNQVGLPVEGIALIIGVDRLLDMVRTAVN 394 Query: 464 VEGDALGAGILHHLNQKATKKGEQELAEVKVEAIPNCKSEEETSPLVTHQNPAGPVAS 521 V GD + ++ KSE E + V + AG VAS Sbjct: 395 VTGDCVATVVI-------------------------AKSEGEFNETVFNNTQAGKVAS 427 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: 352 Number of extensions: 19 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: 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