Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized, see rationale)
to candidate WP_086508845.1 BZY95_RS04845 TRAP transporter large permease
Query= uniprot:Q9KQS1 (453 letters) >NCBI__GCF_002151265.1:WP_086508845.1 Length = 424 Score = 351 bits (901), Expect = e-101 Identities = 175/443 (39%), Positives = 273/443 (61%), Gaps = 21/443 (4%) Query: 3 VALLFILVIGMMIVGVPIAISLGLSSILFLLWHSDASLASVAQTLFNAFAGHYTLLAIPF 62 + L + ++++G+PI SL + L + + + V +F +++L+AIPF Sbjct: 2 ITALLPIFFAVLLLGLPIFASLAFAVFLAIDFFGTTNPVIVPMRMFTGM-NNFSLMAIPF 60 Query: 63 FILASTFMSTGGVAKRIIRFAIAMVGWFRGGLAIASVVACMMFAALSGSSPATVVAIGSI 122 FILA+ M GG++ R+I A A+VGW GGLA A+V++C++F A+SGSSPATVVAIGSI Sbjct: 61 FILAAELMRIGGLSGRLIELAKALVGWVPGGLAAATVLSCLLFGAISGSSPATVVAIGSI 120 Query: 123 VIAGMVKNGYSKEFAAGVICNAGTLGILIPPSIVMVVYSAATNVSVGRMFLGGVVPGLLA 182 + +V GY K FA G+I AGTLG ++PPSI +++Y + T SVGR+F G++P +L Sbjct: 121 MFPALVAAGYDKRFAIGLIATAGTLGPIVPPSIALIIYGSVTGTSVGRLFAAGLLPAILI 180 Query: 183 GLMLIIAIYITARIKNLPKQPFVGWKEALKAAKEASWGLLLVVIILGGIYGGIFTPTEAA 242 +LI + + K + PF +E A K A+WGL L VI+LGGIY GIFTPTE+A Sbjct: 181 ASLLIAYCMVYSSFKGYARAPFPTLREIAAAVKSAAWGLGLPVILLGGIYSGIFTPTESA 240 Query: 243 AVAAVYSFFIANFIYRDMGPFADKTNTKPVLVKVVETFVHKDTKATLYDAGKLTIMLMFI 302 AVA +Y F+ +YR +G ++ TL ++G + L+ I Sbjct: 241 AVACMYGLFVGMVVYRTIG--------------------WRELLGTLRNSGLTSATLLLI 280 Query: 303 IANALILKHVLTEERIPQMITESMLSAGLGPITFLIVVNLILLVGGQFMEPSGLLVIVAP 362 A A +L P + +LS P+ + + N++++V G F++ + +++++P Sbjct: 281 TAGASAFSWLLAITGTPTQLASQVLSLTDHPVQVMALFNVVMIVAGFFLDSASAIIVLSP 340 Query: 363 LVFPIAIALGIDPIHLGIMMVVNMEIGMITPPVGLNLFVTSGVAKMSMMNVVKAALPWVG 422 L+ PIA +G+DP+H GI+ +VN +GMITPPVGLNLFV +++MS++ V +A +P + Sbjct: 341 LLQPIAAQVGVDPVHFGIITLVNFSVGMITPPVGLNLFVAMAISRMSLLEVFRACIPLIV 400 Query: 423 VMFLFLIIVTYVPWVSTWLPTLL 445 +MF+ LI++TYVPW STW+P+L+ Sbjct: 401 MMFIALIVLTYVPWFSTWVPSLI 423 Lambda K H 0.329 0.142 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: 507 Number of extensions: 22 Number of successful extensions: 2 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: 453 Length of database: 424 Length adjustment: 32 Effective length of query: 421 Effective length of database: 392 Effective search space: 165032 Effective search space used: 165032 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 24 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