Align Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized)
to candidate 8500111 DvMF_0874 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::Q8NRL8 (579 letters) >FitnessBrowser__Miya:8500111 Length = 454 Score = 192 bits (487), Expect = 3e-53 Identities = 128/414 (30%), Positives = 210/414 (50%), Gaps = 27/414 (6%) Query: 34 REVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDFA 93 R+ F++R + A +GSAVGLGNIW+FP + NGG +FL+ Y +A L G+P++ + Sbjct: 9 RDGFATRLGVLAATLGSAVGLGNIWKFPALTGQNGGASFLLVYVLATLLVGLPVMISEIM 68 Query: 94 IGHRYRGSAPLAFRRFKKQTE---TIGWIQVGIAFFITIYYAAIIGWAGLYAFKSLNKAW 150 +G R R +A FR+ + + +G+ V AF I +Y + GW Y FKSL+ Sbjct: 69 LGRRARANAVGTFRQLAPKGQPWHLVGFSGVVAAFLIMGFYTDVAGWVFAYIFKSLSGEI 128 Query: 151 GADPDTYFFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAIGVDKGIGRVSMVFM 210 F EA+V D V + ++ + +++++A GV +GI R + V M Sbjct: 129 ATTDPAVAAKAF-----EALVG-DPVQSLLWQWGVLVLISVIIIA-GVAQGIERTTKVLM 181 Query: 211 PLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFSLSVGFGIML 270 P+L+++ + V +++ LP A GL LFTP++ + P V + A G FF LS+G G M Sbjct: 182 PVLLLLLVAVCARSLTLPKAAEGLAFLFTPDFSKI-TPGVILMALGLAFFKLSIGMGTMT 240 Query: 271 TYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGVDEVATSGIGLA 330 TY SY + ++ T + + +LAG+ VF A+ N G ++G L Sbjct: 241 TYGSYFRNDQDIPLTATRVMLCDLTISILAGMAVFPAV----FNFGF----EPSAGPSLL 292 Query: 331 FVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLNRKATAIGVG 390 F+ PA+ +P G +F +FF IA ++ SLLEV V+ + + FG+ RK I Sbjct: 293 FMTIPAVFTSLPGGQVFMVIFFCLTAIAATGAMLSLLEVPVAWLAESFGMPRKRATILTS 352 Query: 391 VVMALLSLGLFSTTS--------GLATLDIMDKFTNNIGIVAVALIAVVSIDWV 436 V +A++ L + S G+ D+ D ++N+ + + + WV Sbjct: 353 VTLAIIGLPATLSMSTMANVKIFGMTVFDLYDFLSSNVLLPVGGIFICLFAGWV 406 Lambda K H 0.325 0.141 0.430 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: 580 Number of extensions: 30 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: 579 Length of database: 454 Length adjustment: 35 Effective length of query: 544 Effective length of database: 419 Effective search space: 227936 Effective search space used: 227936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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