Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate WP_011650499.1 RL_RS03905 carbohydrate ABC transporter substrate-binding protein
Query= uniprot:A8LLL6 (452 letters) >NCBI__GCF_000009265.1:WP_011650499.1 Length = 453 Score = 541 bits (1393), Expect = e-158 Identities = 259/455 (56%), Positives = 325/455 (71%), Gaps = 5/455 (1%) Query: 1 MRHTLHASAAALALSAGMAGAGGHLAFTPGE-GEFNWDSYQAFAEA-TDLSGQDLSIFGP 58 M+ + A AL AG A A L F PG+ +FNW SY F A DL GQ L+IFGP Sbjct: 1 MKKSFLMGVAVAALFAGAASAAD-LKFAPGQDSKFNWKSYDEFKAAHADLKGQPLTIFGP 59 Query: 59 WLAGEADAFSNLVAFFNEATGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGLATTM 118 W + F +++A+F EATG +A Y S++ EQQIVID +AGS P++ V PQPGL + Sbjct: 60 WRGEDEAFFMSVLAYFTEATGIDAKYSSSENYEQQIVIDTQAGSPPNIAVLPQPGLLADL 119 Query: 119 AARGFLTPLPDGTDDWLRENYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVWYIPE 178 A++GFLTPL D W+++NY AG SW+ GTY G + Y F + +VKSLVWY+PE Sbjct: 120 ASKGFLTPLGDDNSKWIKDNYGAGDSWVGYGTYKGKDGKEAFYAFPYKADVKSLVWYVPE 179 Query: 179 NFEDFDYEVPETMEEFKALMDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRTQPPE 238 NFE+ Y++P TMEE AL DQ+V+DG P C+GLGSGGATGWPATDWVED+MLR QPPE Sbjct: 180 NFEEAGYKIPTTMEELHALTDQIVKDGGVPWCIGLGSGGATGWPATDWVEDIMLRMQPPE 239 Query: 239 VYDAWVSNEMPFDDPRVVAAIEEYGSFTRNDDYVVGNANDTASVDFRESPLGLFASPPAC 298 YD W +NE+ F DP VVAAI+E+G F +N YV G AS DFR+SP GLFA PP C Sbjct: 240 AYDKWTTNELKFTDPAVVAAIDEFGKFAKNAKYVDGGVAAVASTDFRDSPKGLFAVPPKC 299 Query: 299 MMHRQASFIPAYFPEGTELGEDADFFYFPAF-EEKDLGRPVLGAGTLFAITNENPAASAF 357 MH QASFIP++FPEGT+LG+DADFFY P F +LG+PVLGAGTL +I ++ AA AF Sbjct: 300 YMHHQASFIPSFFPEGTKLGQDADFFYMPTFASHPELGKPVLGAGTLVSIAKDSKAARAF 359 Query: 358 IEFLKTPFAHEIMMAQDGFLTPFKGANPAAYASDTLRGQGEILTNATTFRFDGSDLMPGG 417 I+FLKTP AHE+ MAQ FLTP+K + AYA+ ++ +G+ILT+ATTFRFDGSDLMPG Sbjct: 360 IDFLKTPIAHEVWMAQSSFLTPYKSVSTEAYANPQMKKEGDILTSATTFRFDGSDLMPGK 419 Query: 418 VGAGTFWTGMVDYSSGAKSAADVASEIQASWESLK 452 +GAG FWTGMVD+ G KSA + A EIQ++W+ +K Sbjct: 420 IGAGAFWTGMVDF-VGGKSAEEAAGEIQSAWDGIK 453 Lambda K H 0.317 0.134 0.413 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: 758 Number of extensions: 41 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: 452 Length of database: 453 Length adjustment: 33 Effective length of query: 419 Effective length of database: 420 Effective search space: 175980 Effective search space used: 175980 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