Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS07235 BWI76_RS07235 hypothetical protein
Query= TCDB::P0AEE5 (332 letters) >FitnessBrowser__Koxy:BWI76_RS07235 Length = 307 Score = 149 bits (376), Expect = 9e-41 Identities = 102/329 (31%), Positives = 180/329 (54%), Gaps = 28/329 (8%) Query: 1 MNKKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLL 60 MN K +++++A ML A A D +GV++ +DDNF++++R A++++ + V+ Sbjct: 1 MNIKKTVVASLIACML-PAVVMAKDISVGVSMALFDDNFLTILRTAMQKEMQK-DGVKAQ 58 Query: 61 MNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRK 120 + D++ D S+Q Q+ + +GV A+ +N VD A ++++A +P++F N+ P + Sbjct: 59 VEDAKGDVSQQLQQVQNFIGQGVDAIIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQAQ 118 Query: 121 ALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEA 180 DK YVG+DS +G +Q + +AK +N G + +L G+ + Sbjct: 119 LT---DKMAYVGSDSVLAGRLQMEALAK--------AMNGKGNV--AILLGDLANESTRD 165 Query: 181 RTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMG 240 RT V +E+ K + +Q TA + A D + W++ + I+ + +NND MA+G Sbjct: 166 RTKGV-EEVVAKYPDIKIVQKQTAKFTRNDAVDVVSNWMT--SGEDIQAIASNNDEMAIG 222 Query: 241 AVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKG 300 A++AL N + I + GVD P+AL ++K+G + T+ DA Q + D A LA+G+ Sbjct: 223 ALQAL-GKNPNHILIAGVDGTPDALQMLKNGKMIATIFQDAKGQGEGAVDAAIKLANGE- 280 Query: 301 AADGTNWKIDNKVVRVPYVGVDKDNLAEF 329 K++ KV+ VPY + KDN+AEF Sbjct: 281 -------KVE-KVIDVPYQLITKDNMAEF 301 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: 275 Number of extensions: 25 Number of successful extensions: 6 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: 307 Length adjustment: 28 Effective length of query: 304 Effective length of database: 279 Effective search space: 84816 Effective search space used: 84816 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:
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