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 5207779 Shew_0300 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::Q8NRL8 (579 letters) >FitnessBrowser__PV4:5207779 Length = 452 Score = 169 bits (429), Expect = 2e-46 Identities = 133/429 (31%), Positives = 208/429 (48%), Gaps = 34/429 (7%) Query: 37 FSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDFAIGH 96 FSSR FI+AA GSAVG+GNIW FP A +GGGAFL+ Y + + G P+L + IG Sbjct: 9 FSSRIGFIMAAAGSAVGVGNIWGFPTQAATHGGGAFLLVYLVLIFLLGYPMLVAELMIGR 68 Query: 97 RYRGSAPLAFRRF------KKQTETIGWIQVGIAFFITIYYAAIIGWAGLYAFKSLNKAW 150 + + A + + +TIG+ + A I +Y+ + GW + + + Sbjct: 69 HGQTNPADAMAKLGSSKLSRNLGKTIGFASIITATLICTFYSILSGWFVSFTLAPIARLV 128 Query: 151 GADPDTYFFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAIGVDKGIGRVSMVFM 210 G + + F + + + ++ +FI+ + ++V+ GV +GI S M Sbjct: 129 GMQDIALWLTSF-SLERNLLFTL---------IFILMV--VLVIRQGVQQGIEAWSKRLM 176 Query: 211 PLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFSLSVGFGIML 270 PLL+ I ++ V + PGA GL+AL P++ + P V I A GQ FFSL+VG G M+ Sbjct: 177 PLLLAILILGVAYILTQPGASQGLNALLVPDFGRIWEPQVLIGALGQTFFSLTVGTGAMM 236 Query: 271 TYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGV---DEVATSGI 327 Y +YL + NL ++S LA + + A+ ++A + GV + D + Sbjct: 237 VYGAYLNRQENLAKLTAYVTLTDTSVAFLAALMIIPAM-YVAQHNGVQIFAADGSLLNAD 295 Query: 328 GLAFVAFPAIINEMPLGGLFG----FLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLNRK 383 L F PA+ + LGGL G +FF +TIAG TS S++EV S + +K + R Sbjct: 296 TLVFTVLPALFDS--LGGLAGQLIAIVFFILMTIAGLTSAISIVEVPTSYMVEKTEIQRH 353 Query: 384 ATAIGVGVVMALLSLGLFSTTSGLATLDIMDKFTNNIGIVAVALIAVVSIDWVLRRIDEF 443 + VG +ALL+ + L L I T +AL + WV R Sbjct: 354 SATYLVGGGIALLATIMVFNFDALFALVI--TLTTERAQPFIALGIALYTGWVWHR---- 407 Query: 444 STHLNAISA 452 ++ L AI+A Sbjct: 408 NSLLKAIAA 416 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: 533 Number of extensions: 34 Number of successful extensions: 4 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: 452 Length adjustment: 35 Effective length of query: 544 Effective length of database: 417 Effective search space: 226848 Effective search space used: 226848 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