Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate WP_045582020.1 AL072_RS00100 TRAP transporter large permease subunit
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >NCBI__GCF_001305595.1:WP_045582020.1 Length = 432 Score = 289 bits (739), Expect = 1e-82 Identities = 148/421 (35%), Positives = 249/421 (59%), Gaps = 5/421 (1%) Query: 1 MALAVFLSSLFGLMLLGMPIAFALMLTGVALMVHLDFFDAQLVAQNMLSGADNYPLMAVP 60 M A+ L LML GMPI+ +L LT ++ + + VA + +G + + +MA+P Sbjct: 1 MNAAIIFGLLLALMLTGMPISISLGLTVLSFLFFMTTVPIDAVALKLFTGIEKFEIMAIP 60 Query: 61 FFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALAT 120 FFILAG + GG+++R+IN A ++VGH GGLG + A + A++SGS+ A A+ + Sbjct: 61 FFILAGNFLTHGGVARRMINFATAMVGHWHGGLGLAGVMACALFAAVSGSSPATVVAIGS 120 Query: 121 LLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTN-----TSISGLFMAGI 175 +++P M G+P AG++ + G + +IPPS+ +++ V T SI +F+AG+ Sbjct: 121 IILPAMVAQGFPKHFGAGIVTTSGALGILIPPSIVMVMYCVATTGHPQAPSIGQMFIAGV 180 Query: 176 VPGLLMGAGLVITWMFVVRGMTVKLQPKASWGERRTALVEGVWALALPVIIIGGLRGGIF 235 VPGL++ L T R PKAS+ +R AL E W L L V+++GG+ GIF Sbjct: 181 VPGLMLALFLGFTTWNRARRFGYPRLPKASFAQRLHALRESFWGLLLIVVVMGGIYSGIF 240 Query: 236 TPTEAAVVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVTLA 295 TPTEAA +AAVY+ VVA+FVY+ + L + +L+ +A ++ ++++ A++ S+++T Sbjct: 241 TPTEAAAMAAVYAFVVAVFVYKDMPLSRVPKVLLDSASMSAMLLYIITNAVLFSFLMTSE 300 Query: 296 DLPQQMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPT 355 +PQ M + + ++ + ++LLA G M+ + +L++ P+L P+A GIDP Sbjct: 301 QIPQNMAAWILDQNMGVWVFLLVVNIILLAAGNFMEPSSIVLIMAPILFPVAMKLGIDPV 360 Query: 356 YFGVMFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVPE 415 +FG++ ++ +G+ HPPV L V G+ ++ + T +WP+LLT L+ L L+ VP Sbjct: 361 HFGILIIVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLIFLGLVTYVPA 420 Query: 416 I 416 I Sbjct: 421 I 421 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: 400 Number of extensions: 21 Number of successful extensions: 4 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: 432 Length adjustment: 32 Effective length of query: 394 Effective length of database: 400 Effective search space: 157600 Effective search space used: 157600 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