Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate CCNA_01515 CCNA_01515 C4-dicarboxylate transporter large subunit
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Caulo:CCNA_01515 Length = 426 Score = 303 bits (776), Expect = 7e-87 Identities = 176/458 (38%), Positives = 264/458 (57%), Gaps = 38/458 (8%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M++ LL ++ LL+IGVP+A ALGL+S L I+ D + VA F+L+AI Sbjct: 1 MELTLLLGLLALLLIIGVPVAFALGLAS-LVTFIFMDIAPV-VAFQRIATGVNVFSLMAI 58 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFI A M G+A R++R + A +G + GGL + V A M+F +SGS+ A+V A+G Sbjct: 59 PFFIFAGDLMQQAGIAERLVRVADAAMGRIRGGLGVVDVGASMMFGGVSGSAVASVSALG 118 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAA--VEVSVGRMFLAGVIP 178 S +I M++ GY ++A V + LGILIPPS M++YAAA V VSV +FLAGV+P Sbjct: 119 STLIPLMKEKGYDADYAVNVTSTSAILGILIPPSHNMIIYAAAAGVSVSVADLFLAGVLP 178 Query: 179 GLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTP 238 G++ G+ L +++A + PKGE+ GW AA+ A+A GLL II GG+ GG+FTP Sbjct: 179 GILTGIFLAAAAWIIAVRRGYPKGEFPGWPAFAAAFASALPGLLTAVIIFGGVLGGVFTP 238 Query: 239 TEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHAD 298 TE++AVA +Y +A VYR +G F Sbjct: 239 TESSAVAVIYTLVIAVIVYRTLG---------------------------------FRGF 265 Query: 299 TRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVIL 358 T A A K T ++ +I +A +L + P+Q+AT + + P++ L+++N+IL Sbjct: 266 TT-AAQNAVKTTAMVMLIIGSAAAFGWLLALLEAPEQLATLLQTLTDNPILILLLINLIL 324 Query: 359 LIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSG 418 LI G FM+ + L+VI +P+ P+A+ G+DP+ GI+M++N+ IG++TPPVG LFV Sbjct: 325 LILGTFMDMAPLIVITSPIFLPVAMATGMDPVQFGIMMMLNLGIGLVTPPVGSVLFVGCA 384 Query: 419 VAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 V + + VR PF LF L+ IT++P ++ LP Sbjct: 385 VGKIKVEQAVRTIWPFYLALFAALMAITFVPALTLTLP 422 Lambda K H 0.329 0.144 0.421 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: 598 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 467 Length of database: 426 Length adjustment: 32 Effective length of query: 435 Effective length of database: 394 Effective search space: 171390 Effective search space used: 171390 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 (21.8 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