Align neutral amino acid transporter A (characterized)
to candidate Echvi_3159 Echvi_3159 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__Cola:Echvi_3159 Length = 449 Score = 188 bits (478), Expect = 3e-52 Identities = 133/453 (29%), Positives = 223/453 (49%), Gaps = 63/453 (13%) Query: 44 LVLLTVSGVLAGAGLGAALRG----LSLSRTQVT--YLAFPGEMLLRMLRMIILPLVVCS 97 L L + +L G G G L +S + +LA PG + L++++MI++PL+V S Sbjct: 24 LWLKVIIALLLGVGFGLLLSPQNGWISKETADIAGNWLALPGVLFLKLVQMIMIPLIVAS 83 Query: 98 LVSGAASLDASCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGS--GAQTLQSSDLGL 155 +++G AS D L +LGG + YF TT+ + ++ L+ I +PG Q L+ + Sbjct: 84 IITGIASNDKDSLKKLGGGVLLYFLGTTIVSVSIGTILSQIFRPGRFLHQQALKEHNEIT 143 Query: 156 EDSGPPPVPKETVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIG 215 S P V++ D NL P N P+ Sbjct: 144 AVSTDEPELSFGVETIPDAISNLLPEN------------------------------PLA 173 Query: 216 TEIEGMNILGLVLFALVLGVALKKLGSEGEDLIR----FFNSLNEATMVLVSWIMWYVPV 271 + + G +L +V+F +++GVA+ L + DL+R +++ E M +V W M VP+ Sbjct: 174 SMVSG-EMLSIVIFTIIIGVAVLSLEN---DLLRPVKLLLSAIQEVCMTVVKWSMLLVPI 229 Query: 272 GIMFLVGSKIVEMKDIIVLVTSLGKYIFASI---LGHVIHGGIVLPLIYF----VFTRKN 324 + L+ L +S+G + + +G V+ G + L + Y + + N Sbjct: 230 AVFGLMAQ----------LTSSVGLSSLSGLTYYVGVVLLGLLFLVIFYLGLIVLLGKAN 279 Query: 325 PFRFLLGLLAPFATAFATCSSSATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAI 384 P FL + AF+T SS+A +P ++ EE VDK IS FI+PIGATVNMDG A+ Sbjct: 280 PMHFLKKIRDVQLLAFSTTSSAAVMPLSLQTAEEKLKVDKTISNFIIPIGATVNMDGTAL 339 Query: 385 FQCVAAVFIAQLNNVELNAGQIFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHD 444 +Q + +FIAQ +E++ I ++VT A+S+G +P GGV+ +A +L ++G+P Sbjct: 340 YQTITTLFIAQAYGLEMSLLNIIVVIVTIVAASIGTPAIPGGGVVILASVLGSVGIPAEG 399 Query: 445 LPLILAVDWIVDRTTTVVNVEGDALGAGILHHL 477 + +I+ V+ ++ T VNV GD + + L Sbjct: 400 IIIIIGVERLLGMFRTAVNVMGDLTACMVFNRL 432 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: 395 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 532 Length of database: 449 Length adjustment: 34 Effective length of query: 498 Effective length of database: 415 Effective search space: 206670 Effective search space used: 206670 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