Align ABC transporter for D-Sorbitol, periplasmic substrate-binding component (characterized)
to candidate WP_086511131.1 BZY95_RS17260 sugar ABC transporter substrate-binding protein
Query= reanno::BFirm:BPHYT_RS16115 (440 letters) >NCBI__GCF_002151265.1:WP_086511131.1 Length = 434 Score = 562 bits (1449), Expect = e-165 Identities = 261/425 (61%), Positives = 329/425 (77%) Query: 14 AGAVACFALSASAATVTIATLNNPDMIELKKLSPEFEKANPDIKLNWVILEENVLRQRAT 73 AG A FA +A A T+T+AT+NN DM+ ++ L+ FE+A+P I++NWV+LEENVLRQR T Sbjct: 10 AGLAAAFATAAQAETITVATVNNNDMVIMQSLTSAFEEAHPGIRVNWVVLEENVLRQRLT 69 Query: 74 TDITTGSGQFDVMTIGAYETPQWGKRGWLTPLTNLPADYDLNDVVKTARDGLSSGGQLYA 133 TDI T GQFDVMTIG YE P W +RGWL L +LP D++K RDGLS G LYA Sbjct: 70 TDIATDGGQFDVMTIGTYEAPIWAERGWLVALDDLPEASQEEDLLKPVRDGLSHNGSLYA 129 Query: 134 LPFYVESSMTYYRKDLFEKAGLKMPDQPTYDQIKQFADKLTDKANGIYGICLRGKAGWGE 193 LPFY ESSM YYR DLFE+AG++MP+QP++++++++A +L D AN + GICLRGK GWGE Sbjct: 130 LPFYAESSMLYYRTDLFEEAGIEMPEQPSWEEVREWAAELHDPANQLAGICLRGKPGWGE 189 Query: 194 NMAYGTTVVNTFGGRWFDEKWNAQLTSPEWKKAMTFYVDLLKKDGPPGASSNGFNENLTL 253 NMA+ +T+VNTFGGRWFDE+WN +L SP W++A+ FYVDLL GPPGASSNGFNENL L Sbjct: 190 NMAFVSTLVNTFGGRWFDEEWNPELDSPAWQEAIGFYVDLLGNYGPPGASSNGFNENLAL 249 Query: 254 MSSGKCAMWIDATVAAGMLYNKQQSQIADKVGFAAAPVAVTPKGSHWLWAWALAIPKSSK 313 S G CAMW+DAT AAG LYN +SQ+AD++GFA APVA TPKG+HWLW+WALAIP SS+ Sbjct: 250 FSRGNCAMWVDATSAAGKLYNPAESQVADRLGFAPAPVAETPKGAHWLWSWALAIPASSE 309 Query: 314 QADAAKKFITWATSKQYIELVAKDEGWASVPPGTRKSTYARAEYKQAAPFGDFVLKAIET 373 + +AA+ F+TWATS++YIELV + +GW SVPPGTR+STYA Y++ APF FVL AI + Sbjct: 310 KQEAAQTFLTWATSQEYIELVGETQGWTSVPPGTRESTYANENYQREAPFAGFVLDAINS 369 Query: 374 ADPEHPTLKPVPYTGVQFVGIPEFQSFGTVVGQSISGAIAGQMTIDQALAAGNATADRAV 433 ADP TL+P PY GVQFVGIPEFQS GT VGQ+I+ A+ G ++QAL R + Sbjct: 370 ADPTDSTLEPSPYVGVQFVGIPEFQSIGTQVGQTIAAALTGDTGVEQALQNAQRATARTM 429 Query: 434 KQAGY 438 ++AGY Sbjct: 430 QRAGY 434 Lambda K H 0.315 0.130 0.396 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: 630 Number of extensions: 19 Number of successful extensions: 1 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: 440 Length of database: 434 Length adjustment: 32 Effective length of query: 408 Effective length of database: 402 Effective search space: 164016 Effective search space used: 164016 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: 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