Align The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized)
to candidate GFF2680 HP15_2624 sodium-dependent transporter family protein
Query= TCDB::Q8RHM5 (438 letters) >FitnessBrowser__Marino:GFF2680 Length = 470 Score = 184 bits (466), Expect = 7e-51 Identities = 132/427 (30%), Positives = 205/427 (48%), Gaps = 46/427 (10%) Query: 8 FQSKIGFILTCVGSAVGMANIWAFPYRVGKYGGAVFLLIYFMFIALFSYVGLSAEYLIGR 67 + S++ FIL GSAVG+ NIW FPY G+ GG F+L+Y + IA+ + AE +IGR Sbjct: 25 WSSRLAFILAATGSAVGLGNIWKFPYVTGENGGGAFVLVYLLCIAVVGIPIMMAEVMIGR 84 Query: 68 RAETGTLGSYEY---------AWKDVGKGKLGYGLAYIPLLGSMSIAIGYAVIAAWVLRT 118 R + S AWK VG I +L I Y+VI W + Sbjct: 85 RGGRSPVKSLSLIAEHDRLKPAWKLVGA---------IGILAGFLILSFYSVIGGWAISY 135 Query: 119 FGAAVTGKIL--EVDTA-QFFGEAVTGNFVIMPWHIAVIVLTLLTLFAGAKS-IEKTNKI 174 G +G++ DT F ++ ++ WH + + ++ + G +S +E+ I Sbjct: 136 VGTTASGQLAGQSADTVGAVFSGLLSDPTKLLAWHTLFMAMVMVVVVRGVRSGLERAVSI 195 Query: 175 MMPAFFVLFFILAVRVAFLPGAI-EGYKYLFVPDWSYLSNVETWINAMGQAFFSLSITGS 233 +MPA FVL I+ V A G + +LF PD+S L+ + A+G AFF+LS+ + Sbjct: 196 LMPALFVLLLIV-VGYAMTTGHFGQAAAFLFQPDFSKLTTSGILV-ALGHAFFTLSLGMA 253 Query: 234 GMIVCGAYLDKKEDIINGALQTGVFDTIAAMIAAFVVIPASFAFGYPASAGPSLMFMTIP 293 M+ G+YL K I ++ V DT A++A + P FA G AGP L+F T+P Sbjct: 254 VMMAYGSYLPKNISIAKTSITVSVIDTGVALLAGLAIFPIVFANGLEPGAGPGLIFQTLP 313 Query: 294 EVFKQMPFGQLLAILFFVSVVFAAISSLQNMFEVVGESIQTRFKMTRKSVIVLLGIIALV 353 F QMP G L LFFV ++FAA +S ++ E + E ++ R M R + G + Sbjct: 314 LAFGQMPMGSLFGTLFFVLLIFAAWTSGISLLEPIVEWLEERKGMNRTVSTLGAGFVCWG 373 Query: 354 IGIF----------IEPENKVGPWMDVVTIY----------IIPFGAVLGAISWYWILKK 393 +GI P V P ++ TI+ ++P G +L A+ W++ + Sbjct: 374 LGIASILSLNLWSDFAPLGFV-PMLEGKTIFDLLDFFTANIMLPLGGLLVALFAGWVMSR 432 Query: 394 ESYMEEL 400 ++ EL Sbjct: 433 QAMEREL 439 Lambda K H 0.328 0.143 0.434 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: 587 Number of extensions: 33 Number of successful extensions: 5 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: 438 Length of database: 470 Length adjustment: 33 Effective length of query: 405 Effective length of database: 437 Effective search space: 176985 Effective search space used: 176985 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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