Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate WP_017617377.1 CDO52_RS08520 carbohydrate ABC transporter substrate-binding protein
Query= uniprot:A8LLL6 (452 letters) >NCBI__GCF_002263495.1:WP_017617377.1 Length = 452 Score = 266 bits (679), Expect = 1e-75 Identities = 157/435 (36%), Positives = 218/435 (50%), Gaps = 19/435 (4%) Query: 18 MAGAGGHLAFTPGEGEFNWDSYQAFAEATDLSGQDLSIFGPWLAGEADAFSNLVAFFNEA 77 ++G GG A G G + FAE D+ G + I+ E + F+E Sbjct: 30 LSGTGGTSAERGGAG------CEPFAEWADVEGGTVDIYASIRDEEGERMQRAWKNFSEC 83 Query: 78 TGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGLATTMAARGFLTPLPDGTDDWLRE 137 TG N Y GS E Q+ + + G+APD+ FPQPGL + G PLP+ +E Sbjct: 84 TGINIRYEGSGEFEAQVQVKIDGGNAPDIAFFPQPGLLSRFVESGDALPLPESVAKRAQE 143 Query: 138 NYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVWYIPENFEDFDYEVPETMEEFKAL 197 Y + W+ Y + G +LYG NVKS VWY P F + YE P T ++ L Sbjct: 144 GYP--EDWLQ---YVEHDG--KLYGTPLGANVKSFVWYSPGFFTENGYETPTTWDDLIKL 196 Query: 198 MDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRTQPPEVYDAWVSNEMPFDDPRVVA 257 D M +DG P C G+ SG ATGWP TDW+E++MLR P+VYD W+ +E+PFDDP+V Sbjct: 197 SDAMADDGVKPWCAGIESGEATGWPVTDWLENVMLREHGPDVYDQWIDHEIPFDDPKVAT 256 Query: 258 AIEEYGSFTRNDDYVVGNANDTASVDFRES-PLGLFASPPACMMHRQASFIPAYFPEGTE 316 A++ G RN DYV G S+ S G+ C M+ SF A +PEGTE Sbjct: 257 ALDRVGDILRNPDYVNGGHGGVKSIATTSSQDGGIPILEDKCGMYLMGSFYAAQWPEGTE 316 Query: 317 LGEDADFFYF--PAFEEKDLGRPVLGAGTLFAITNENPAASAFIEFLKTPFAHEIMMAQD 374 + ED D F F P +E ++G PVLG G A ++ P A E+L T + Sbjct: 317 IAEDGDVFAFNLPTIDE-EIGTPVLGGGEFTAAFSDRPEVVAVQEYLATVDYANRRAQEG 375 Query: 375 GFLTPFKGANPAAYASDTLRGQGEILTNA-TTFRFDGSDLMPGGVGAGTFWTGMVDYSSG 433 + + K + A + R E+L + T FR+DG D MP VG+GTFW M ++ +G Sbjct: 376 AWFSAHKELDLNALDNPNDRFAAELLRDPDTVFRWDGGDYMPAAVGSGTFWRAMTNWING 435 Query: 434 AKSAADVASEIQASW 448 + DV ++ SW Sbjct: 436 S-DTEDVLGYVEQSW 449 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: 743 Number of extensions: 52 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: 452 Length adjustment: 33 Effective length of query: 419 Effective length of database: 419 Effective search space: 175561 Effective search space used: 175561 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