Align The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized)
to candidate 8500111 DvMF_0874 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::Q8RHM5 (438 letters) >FitnessBrowser__Miya:8500111 Length = 454 Score = 194 bits (493), Expect = 5e-54 Identities = 136/445 (30%), Positives = 221/445 (49%), Gaps = 25/445 (5%) Query: 8 FQSKIGFILTCVGSAVGMANIWAFPYRVGKYGGAVFLLIYFMFIALFSYVGLSAEYLIGR 67 F +++G + +GSAVG+ NIW FP G+ GGA FLL+Y + L + +E ++GR Sbjct: 12 FATRLGVLAATLGSAVGLGNIWKFPALTGQNGGASFLLVYVLATLLVGLPVMISEIMLGR 71 Query: 68 RAETGTLGSYEYAWKDVGKGKLGYGLAYIPLLGSMSIAIGYAVIAAWVLRTFGAAVTGKI 127 RA +G++ KG+ + + + ++ + I Y +A WV +++G+I Sbjct: 72 RARANAVGTFRQL---APKGQPWHLVGFSGVVAAFLIMGFYTDVAGWVFAYIFKSLSGEI 128 Query: 128 LEVD---TAQFFGEAVTGNFV-IMPWHIAVIVLTLLTLFAG-AKSIEKTNKIMMPAFFVL 182 D A+ F EA+ G+ V + W V+VL + + AG A+ IE+T K++MP +L Sbjct: 129 ATTDPAVAAKAF-EALVGDPVQSLLWQWGVLVLISVIIIAGVAQGIERTTKVLMPVLLLL 187 Query: 183 FFILAVRVAFLPGAIEGYKYLFVPDWSYLSNVETWINAMGQAFFSLSITGSGMIVCGAYL 242 + R LP A EG +LF PD+S ++ + A+G AFF LSI M G+Y Sbjct: 188 LVAVCARSLTLPKAAEGLAFLFTPDFSKITP-GVILMALGLAFFKLSIGMGTMTTYGSYF 246 Query: 243 DKKEDIINGALQTGVFDTIAAMIAAFVVIPASFAFGYPASAGPSLMFMTIPEVFKQMPFG 302 +DI A + + D +++A V PA F FG+ SAGPSL+FMTIP VF +P G Sbjct: 247 RNDQDIPLTATRVMLCDLTISILAGMAVFPAVFNFGFEPSAGPSLLFMTIPAVFTSLPGG 306 Query: 303 QLLAILFFVSVVFAAISSLQNMFEVVGESIQTRFKMTRKSVIVLLGIIALVIGI-----F 357 Q+ ++FF AA ++ ++ EV + F M RK +L + +IG+ Sbjct: 307 QVFMVIFFCLTAIAATGAMLSLLEVPVAWLAESFGMPRKRATILTSVTLAIIGLPATLSM 366 Query: 358 IEPENKVGPWMDVVTIY-------IIPFGAVLGAISWYWILKKESYMEELNQGSKVTRSE 410 N M V +Y ++P G + + W+ + EL+ ++ Sbjct: 367 STMANVKIFGMTVFDLYDFLSSNVLLPVGGIFICLFAGWVWGAANVKTELSNRGQLLNGP 426 Query: 411 I---YHNVGKYVYVPLVLVVFVLGV 432 I + V ++V LVL+V + G+ Sbjct: 427 IIAAFLTVVRWVSPVLVLLVLLKGL 451 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: 498 Number of extensions: 26 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: 454 Length adjustment: 32 Effective length of query: 406 Effective length of database: 422 Effective search space: 171332 Effective search space used: 171332 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