Align The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized)
to candidate 206527 DVU1092 sodium-dependent symporter family protein
Query= TCDB::Q8RHM5 (438 letters) >MicrobesOnline__882:206527 Length = 453 Score = 190 bits (482), Expect = 9e-53 Identities = 135/448 (30%), Positives = 216/448 (48%), Gaps = 31/448 (6%) Query: 8 FQSKIGFILTCVGSAVGMANIWAFPYRVGKYGGAVFLLIYFMFIALFSYVGLSAEYLIGR 67 F +++G + +GSAVG+ NIW FP G+ GGA FLL+Y + L + +E ++GR Sbjct: 11 FATRLGVLAATLGSAVGLGNIWKFPALTGQNGGATFLLVYIIATLLVGLPVMISEIMLGR 70 Query: 68 RAETGTLGSYEYAWKDVG-KGKLGYGLAYIPLLGSMSIAIGYAVIAAWVLRTFGAAVTGK 126 +A+ + +Y +++G KG+ + ++ ++ I Y +A WV A++G Sbjct: 71 KAKANAVRTY----RELGPKGQPWSLIGISGVIAAVLIMGFYTDVAGWVFAYIFKAMSGS 126 Query: 127 ILEVDTA---QFFGEAVTGNFVIMPWHIAVIVLTLLTLFAGAKS-IEKTNKIMMPAFFVL 182 I D A + F V + W V+ L + G S IE+T KI+MP +L Sbjct: 127 IATTDPAVAKEAFVALVGSPTQSLMWQWIVLALVSAIILGGVSSGIERTTKILMPVLLLL 186 Query: 183 FFILAVRVAFLPGAIEGYKYLFVPDWSYLSNVETWINAMGQAFFSLSITGSGMIVCGAYL 242 ++ R LP A EG +LF PD+S ++ + A+G AFF LSI M G+Y Sbjct: 187 LCVVCARSLTLPKAAEGLAFLFTPDFSKITG-GVILMALGLAFFKLSIGMGTMTTYGSYF 245 Query: 243 DKKEDIINGALQTGVFDTIAAMIAAFVVIPASFAFGYPASAGPSLMFMTIPEVFKQMPFG 302 ++I A + + D +++A + PA F FG+ SAGPSL+FMTIP VF MP G Sbjct: 246 RDDQNIPVTAARVMLCDLSISILAGVAIFPAVFNFGFEPSAGPSLLFMTIPAVFASMPGG 305 Query: 303 QLLAILFFVSVVFAAISSLQNMFEVVGESIQTRFKMTRKSVIVLLGIIALVIGIFIEPE- 361 QL ++FF AA ++ ++FEV + FKM+R + ALV+G+ P Sbjct: 306 QLFTVIFFCLTAIAATGAMLSLFEVPVAWLVEEFKMSRAKATI---GTALVLGVMGAPAT 362 Query: 362 --------------NKVGPWMDVVTIYIIPFGAVLGAISWYWILKKESYMEELNQGSKVT 407 N + V + ++P G + I W+ + E L+ G + Sbjct: 363 LSMSVLGDFKMFGLNMFDLYDFVSSNILLPVGGIFICIFAGWVWGSKRTRELLSNGGHLD 422 Query: 408 RSEIYHN---VGKYVYVPLVLVVFVLGV 432 + + V K+V LV +V + G+ Sbjct: 423 NAAVVSGFLFVVKWVSPVLVTIVLLNGL 450 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: 510 Number of extensions: 29 Number of successful extensions: 3 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: 453 Length adjustment: 32 Effective length of query: 406 Effective length of database: 421 Effective search space: 170926 Effective search space used: 170926 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