Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate GFF2033 PGA1_c20660 TRAP transporter, subunit DctM
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >FitnessBrowser__Phaeo:GFF2033 Length = 467 Score = 244 bits (623), Expect = 4e-69 Identities = 145/456 (31%), Positives = 244/456 (53%), Gaps = 41/456 (8%) Query: 1 MALAVFLSSLFGLMLLGMPIAFALMLTGVA-LMVHLDFFDAQLVAQNMLSGADNYPLMAV 59 M + + S + GL+L+G+PIA AL L+ L+++ D A + + ++ L+A+ Sbjct: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 Query: 60 PFFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALA 119 PFFILA M GG+++RII +++ VGH+ GGL + A ++ A+LSGS+ A A+ Sbjct: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 Query: 120 TLLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGL 179 +++I MR GY +AG+I + G + +IPPS+ +++ S+ +F+AG++PGL Sbjct: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 Query: 180 LMGAGLVITWMFVVRGMTVKLQPKA---SWGERRTALVEGVWALALPVIIIGGLRGGIFT 236 + G L++T + + VK PK WGE + L L II+GG+ GGIFT Sbjct: 181 MAGLMLMVTIYVMAK---VKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFT 237 Query: 237 PTEAAVVAAVYSLVVALFVYRQV-------------------------TLKDLVP----- 266 PTEAA VA+VY+ VA FVYR + T+ +P Sbjct: 238 PTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHA 297 Query: 267 ----LLVQAARTTSTVMFLCAAALVSSYMVTLADLPQQMNEMLAPLLHEPKLLMVAITLL 322 L +A + T T++F+ A AL+ +++T +PQQ+ + P + ++ + ++ Sbjct: 298 DTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVI 357 Query: 323 LLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYFGVMFVLTGTLGLIHPPVCTVLNVVC 382 LL G M+ + ++++ P++ P+A GIDP + G++ V+ +G+I PPV L V Sbjct: 358 LLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTS 417 Query: 383 GVARISLESATRGIWPFLLTYLLLLCLLIAVPEIVT 418 GVA + + + R PFL + L ++ +P I T Sbjct: 418 GVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWIST 453 Lambda K H 0.328 0.142 0.420 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: 464 Number of extensions: 28 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: 426 Length of database: 467 Length adjustment: 32 Effective length of query: 394 Effective length of database: 435 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