Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 152 bits (385), Expect = 1e-41 Identities = 100/221 (45%), Positives = 130/221 (58%), Gaps = 17/221 (7%) Query: 92 VGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFAVFLGLPRADN 151 V + + +I+GI R + N L L+ V + L +F +G P + Sbjct: 204 VAVFVLSIIGIFV-FRRYAKNLLFNTGKLLPVGRISLAIFFVPTLLAFFV--MGRPIGLD 260 Query: 152 KISLGGFI---GLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQW 208 LGGF G++ G + AL L YTGAFIAE VR GI +VSKGQ Sbjct: 261 YPELGGFNFRGGINIRGTLI----------ALWFALALYTGAFIAENVRAGILAVSKGQT 310 Query: 209 EAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPDIY-FVASTT 267 EA +LG+ P+ IM L+I PQALRVIIPP+ SQYLNLTKNSSLA AIGY D+ + T Sbjct: 311 EAAAALGMRPNRIMSLIILPQALRVIIPPVISQYLNLTKNSSLAAAIGYMDLTGTLGGVT 370 Query: 268 FNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQIKER 308 NQTG++ E +LLLML YL +SL+IS +MN +N V++KER Sbjct: 371 LNQTGRSFECVLLLMLFYLLISLSISALMNLYNNAVKLKER 411 Score = 114 bits (284), Expect = 5e-30 Identities = 62/138 (44%), Positives = 82/138 (59%) Query: 11 DNRFWYIAGQLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYK 70 D R+ Q IAL F L+ N NL LG F FL Q AS++I +TLI Y Sbjct: 26 DTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFLGQPASYEIDQTLIPYT 85 Query: 71 PTDTYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTP 130 TDT+ A +VGL+N+L +AF+G I TI G+LAG+ RLS NWLV + VYVEIFRN P Sbjct: 86 STDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIP 145 Query: 131 LLLQLLFWYFAVFLGLPR 148 +L+ ++ + LP+ Sbjct: 146 VLIWIVIISAVMSQALPQ 163 Lambda K H 0.328 0.143 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: 360 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 308 Length of database: 411 Length adjustment: 29 Effective length of query: 279 Effective length of database: 382 Effective search space: 106578 Effective search space used: 106578 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: 49 (23.5 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