Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate SM_b20712 SM_b20712 rhizopine uptake ABC transporter substrate-binding protein precursor
Query= TCDB::P0AEE5 (332 letters) >lcl|FitnessBrowser__Smeli:SM_b20712 SM_b20712 rhizopine uptake ABC transporter substrate-binding protein precursor Length = 309 Score = 160 bits (404), Expect = 5e-44 Identities = 119/339 (35%), Positives = 179/339 (52%), Gaps = 42/339 (12%) Query: 4 KVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMND 63 K L MA +L AAHA IGV++ +DDNF++V+R +++ AK V+L + D Sbjct: 2 KKFFLGTAMA-VLMSTAAHAET--IGVSMALFDDNFLTVLRSGMQEYAKTLDGVELQVED 58 Query: 64 SQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALD 123 +QND +KQ QI +A GV A+ +N VD A + + A +P+V+ N+EP +D Sbjct: 59 AQNDVAKQQSQIQNFIAAGVDAIIVNPVDTDATAAMSKIAADAGIPLVYVNREPVN--VD 116 Query: 124 SY-DKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEART 182 + DK +V ++ +ESG +Q I K G+ + V++ GE + A RT Sbjct: 117 TLPDKQAFVASNEQESGTLQTKEICKMLG----------GKGKAVVMMGELSNQAARMRT 166 Query: 183 TYVIKELND-------KGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANND 235 K+++D KGI E ++ TA W Q D M WLS + + VI+NND Sbjct: 167 ----KDIHDVIATDECKGI--EIVEEQTANWSRTQGSDLMTNWLSA--GLEFDAVISNND 218 Query: 236 AMAMGAVEALKAHNKS--SIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAK 293 MA+GA++ALKA +S S+ + G+DA +ALA + +G L TV +A Q K + D A Sbjct: 219 EMAIGAIQALKAAGRSMDSVVIGGIDATQDALAAMAAGDLDVTVFQNAAGQGKGSVDAAL 278 Query: 294 NLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEFSKK 332 LA G+ K V +P+ V KDNLA++ K Sbjct: 279 KLAKGEPV---------EKKVYIPFELVTKDNLAQYQTK 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: 15 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: 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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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