Align Maltodextrin-binding protein (characterized, see rationale)
to candidate WP_086508157.1 BZY95_RS01095 maltose/maltodextrin ABC transporter substrate-binding protein MalE
Query= uniprot:Q9RHZ6 (427 letters) >NCBI__GCF_002151265.1:WP_086508157.1 Length = 395 Score = 164 bits (416), Expect = 3e-45 Identities = 104/363 (28%), Positives = 176/363 (48%), Gaps = 14/363 (3%) Query: 54 GQTITVWSWQTGPELQDVKQIAAQWAKAHGDKVIVVDQSSNPKGFQFYATAARTGKGPDV 113 G +T+W ++++A Q+A G +V +V+ + FQ AA +G+GPD+ Sbjct: 29 GDRLTIWMGDN-KGYDGIREVARQFADDTGIEVRIVNPDNLTDRFQ---QAAGSGQGPDI 84 Query: 114 VFGMPHDNNGVFAEEGLMAPVPSGVLNTGLYAPNTIDAIKVNGTMYSVPVSVQVAAIYYN 173 V HD G +A+ GL+APV Y T DA +G Y P+SV+ + YN Sbjct: 85 VI-WAHDRIGEWAQSGLLAPVSPSSDFRERYFDFTWDATLWSGEHYGYPISVEALGLIYN 143 Query: 174 KKLVPQPPQTWAEFVK------DANAHGFMYDQANLYFDYAIIGGYGGYVFKDNNGTLDP 227 K LV PP+++AE + + ++D Y+ + ++ GGY F+ D Sbjct: 144 KALVETPPESFAELAQLDAELAEQGRKAILFDYGEPYYGWTLLAANGGYPFRRTEEGFDV 203 Query: 228 NNIGLDTPGAVQAYTLMRDMVSKYHWMTPSTNGSIAKAEFLAGKIGMYVSGPWDTADIEK 287 ++IG++ GA+Q L+ +++ + T+ SI F G++ +SGPW +++E+ Sbjct: 204 DDIGVNNEGALQGAELLVELIES-GVLPRGTDYSIMDTRFNRGEVAAMISGPWAWSNLEQ 262 Query: 288 AKIDFGVTPWPTLPNGKHATPFLGVITAFVNKESKTQAADWSLVQALTSAQAQQMYFRDS 347 + ID+GV P + + A P GV+ A +N S ++ ++ F Sbjct: 263 SGIDYGVALLPKVGE-ERAKPMFGVMAAMINTASPNDFLAVEFLENYLLSEEGMRTFNSD 321 Query: 348 QQIPALLSVQRSSAVQSSPTFKAFVEQLRYAVPMPNIPQMQAVWQAMS-ILQNIIAGKVS 406 + A+ + ++S P A +E +PMPNIP+M A W AM LQNI +G+ S Sbjct: 322 STLGAVAHIAYQQELESDPNIAATLENAELGMPMPNIPEMGAFWAAMEPALQNIGSGRQS 381 Query: 407 PEQ 409 P + Sbjct: 382 PRE 384 Lambda K H 0.315 0.130 0.392 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: 438 Number of extensions: 31 Number of successful extensions: 6 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: 427 Length of database: 395 Length adjustment: 31 Effective length of query: 396 Effective length of database: 364 Effective search space: 144144 Effective search space used: 144144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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