Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate HSERO_RS04250 HSERO_RS04250 C4-dicarboxylate ABC transporter permease
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >FitnessBrowser__HerbieS:HSERO_RS04250 Length = 426 Score = 305 bits (780), Expect = 2e-87 Identities = 157/415 (37%), Positives = 254/415 (61%), Gaps = 1/415 (0%) Query: 2 ALAVFLSSLFGLMLLGMPIAFALMLTGVALMVHLDFFDAQLVAQNMLSGADNYPLMAVPF 61 AL +F+ LF LML GMPI+ +L LT + + + Q VA + +G + + +MA+PF Sbjct: 3 ALIIFVL-LFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIPF 61 Query: 62 FILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALATL 121 FILAG + GG+++R+IN A S+VGH GGL + A + A++SGS+ A A+ ++ Sbjct: 62 FILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSI 121 Query: 122 LIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGLLM 181 ++P M G+P AG+I + G + +IPPS+ +++ V+TNTS+ LFMAG+VPGLL+ Sbjct: 122 ILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLL 181 Query: 182 GAGLVITWMFVVRGMTVKLQPKASWGERRTALVEGVWALALPVIIIGGLRGGIFTPTEAA 241 L +T F+ R KA+W ER A + W L L VI++GG+ G+FTPTEAA Sbjct: 182 AFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEAA 241 Query: 242 VVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVTLADLPQQM 301 +AAVY+ +A+FVY+ +TLK + +L+ +A ++ ++++ A++ S++VT ++PQ M Sbjct: 242 AMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQAM 301 Query: 302 NEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYFGVMF 361 + P ++ + +LLL G VM+ + +L+L P+L P+A GIDP +FG++ Sbjct: 302 AAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGILI 361 Query: 362 VLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVPEI 416 V+ +G+ HPPV L V G+ ++ + T + P+LLT L L L+ P + Sbjct: 362 VVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPAL 416 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: 18 Number of successful extensions: 3 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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