Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate GFF2732 HP15_2676 proton/sodium-glutamate symport protein
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Marino:GFF2732 Length = 426 Score = 202 bits (515), Expect = 1e-56 Identities = 123/398 (30%), Positives = 227/398 (57%), Gaps = 13/398 (3%) Query: 1 MKLFKNLTVQVITAVIIGVIVGLVWPD----VGKEMKPLGDTFINAVKMVIAPIIFFTIV 56 +K+ + + +IT ++G VGLV P+ +G + G F+ ++M++ P++ ++V Sbjct: 7 LKVLIGMFLGLITGTLLGPSVGLVEPETGTLIGNWLAFPGQLFLATIQMIVIPLVIASVV 66 Query: 57 LGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPG---AGLDYSKLEKGDV 113 G+A D++++ K+G + +F + T +A IGL++ +++ PG AGL + + G+ Sbjct: 67 RGLAAGEDLEQLRKLGLRVTGFFVITTAMAASIGLWIGDLINPGRMMAGLG-TPVAAGEN 125 Query: 114 SQYTQNGGQGIDWI-EFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALG-EKGKSV 171 S + G+D + + + ++P N +DA +G +LQV+ FSI+ G+ L ++ EK + + Sbjct: 126 SVPVASM-PGVDELPKTLIGLLPGNPLDAMVEGQMLQVVIFSIIVGIALVSMAPEKSRPM 184 Query: 172 IDFFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFV 231 +D D + + ++ + MR API FG MA G ++ +AS + +V + + + Sbjct: 185 LDLLDSLQQICMTVVRWAMRLAPIAVFGLMAQLTTTLGFRAMLGMASYVATVIAGLLVLL 244 Query: 232 FVALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKME-RYGCSKSVVGLV 290 V + I+ L G S +L+ +D LL+ TSSS +V+P + E + G SV V Sbjct: 245 GVYMLILKLLAGQSPVRFLKDTRDVLLLAFSTSSSAAVMPLSIRTAEDKLGVRPSVSQFV 304 Query: 291 IPTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIV 350 IP G + N++GT++Y ++AT+FLAQV+G+DLS+G ++ + + S G+ G G ++ Sbjct: 305 IPLGATINMNGTALYQAVATIFLAQVYGIDLSMGSMALVVAMAVGASIGSPATPGVGIVI 364 Query: 351 LASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGN 388 LA L + IP G+AL++GVDR + R +N+ G+ Sbjct: 365 LAMVLQTVG-IPPSGIALIMGVDRILDMCRTAINVTGD 401 Lambda K H 0.326 0.143 0.408 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: 434 Number of extensions: 25 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: 421 Length of database: 426 Length adjustment: 32 Effective length of query: 389 Effective length of database: 394 Effective search space: 153266 Effective search space used: 153266 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 (21.6 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