Align neutral amino acid transporter A (characterized)
to candidate 5209774 Shew_2227 sodium:dicarboxylate symporter (RefSeq)
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__PV4:5209774 Length = 439 Score = 219 bits (559), Expect = 1e-61 Identities = 138/427 (32%), Positives = 222/427 (51%), Gaps = 46/427 (10%) Query: 51 GVLAGAGLGAALRGLSLSRTQVT--YLAFPGEMLLRMLRMIILPLVVCSLVSGAASL-DA 107 G+L G L + G +T L G + + L+M+++PLV SLV G SL D Sbjct: 22 GILTGLLLRSFFPGSEFIEEYITNGLLNVVGSIFISSLQMLVVPLVFISLVCGTCSLSDP 81 Query: 108 SCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKET 167 S LGRLGG +A++ TT A ++A+ +A ++ PG+ + ++ ++++ Sbjct: 82 SSLGRLGGKTIAFYLFTTAIALSMAILVALLVHPGNASLAAENMQYSVKEA--------- 132 Query: 168 VDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLV 227 S D+ NL P N PI EG N+L ++ Sbjct: 133 -PSLSDVLINLVPRN------------------------------PIQAMTEG-NMLQII 160 Query: 228 LFALVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMKDI 287 +FA++ G A+ +G G+ + FN LNE M +V+ IM P GI L+G + + Sbjct: 161 IFAVIFGFAISHIGERGKRVSALFNDLNEVIMRVVTLIMQLAPYGIFALMGKLALTLG-- 218 Query: 288 IVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATCSSSA 347 + S+ KY + ++H + P++ +F+ +PF F+ + AF+T SS+A Sbjct: 219 LETFESVVKYFMVVLAVLLVHAFVSYPVLLKLFSGLSPFTFIRKMRDVQLFAFSTASSNA 278 Query: 348 TLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQIF 407 TLP ++ E GVD +++ F LP+GAT+NMDG AI Q VA VFIAQ+ ++L Sbjct: 279 TLPVTLETSEHRLGVDNKVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYA 338 Query: 408 TILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVNVEGD 467 ++VTAT +S+G AGVP G++ +A++L +GLP + LI+ VD ++D T VNV GD Sbjct: 339 MVVVTATLASIGTAGVPGVGLIMLAMVLNQVGLPVEGIALIMGVDRLLDMVRTAVNVTGD 398 Query: 468 ALGAGIL 474 ++ I+ Sbjct: 399 SVATVII 405 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: 322 Number of extensions: 8 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: 439 Length adjustment: 34 Effective length of query: 498 Effective length of database: 405 Effective search space: 201690 Effective search space used: 201690 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