Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_037155072.1 RHSP_RS28510 sugar ABC transporter substrate-binding protein
Query= TCDB::P0AEE5 (332 letters) >NCBI__GCF_000359745.1:WP_037155072.1 Length = 309 Score = 159 bits (401), Expect = 1e-43 Identities = 122/339 (35%), Positives = 177/339 (52%), Gaps = 42/339 (12%) Query: 4 KVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMND 63 K L + MA +L AAHA IGV++ +DDNF++V+R ++ AK V L + D Sbjct: 2 KKFILGSAMA-LLLSTAAHAQT--IGVSMALFDDNFLTVLRNGMQDYAKGMSGVTLQVED 58 Query: 64 SQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALD 123 +QND +KQ QI +A V A+ +N VD A + + A +P+V+ N+EP+ +D Sbjct: 59 AQNDVAKQQSQIQNFIASKVDAIIVNPVDTDATAAISKLAADAKIPLVYVNREPAN--VD 116 Query: 124 SY-DKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEART 182 S DK +V ++ +ESG ++ + + G+ + V++ GE + A RT Sbjct: 117 SLPDKQAFVASNEQESGTLETKEVCRILG----------GKGKAVVMMGELSNQAARMRT 166 Query: 183 TYVIKELND-------KGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANND 235 K+++D KGIK Q Q TA W Q D M WLS + + + VI+NND Sbjct: 167 ----KDVHDVLATDGCKGIKIVQEQ--TANWQRTQGADLMTNWLS--SGLEFDAVISNND 218 Query: 236 AMAMGAVEALKAHNK--SSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAK 293 MA+GA++ALKA K I V GVDA +ALA +++G L TV DA Q K D A Sbjct: 219 EMAIGAIQALKAAGKPMDKIVVAGVDATQDALAAMQAGDLKVTVFQDAAGQGKGAVDAAL 278 Query: 294 NLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEFSKK 332 LA G KID KV +P+ V N+ +F KK Sbjct: 279 KLAKGD--------KIDKKVY-IPFQLVTPTNVKDFVKK 308 Lambda K H 0.313 0.129 0.363 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: 238 Number of extensions: 13 Number of successful extensions: 4 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: 332 Length of database: 309 Length adjustment: 28 Effective length of query: 304 Effective length of database: 281 Effective search space: 85424 Effective search space used: 85424 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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