Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_085545417.1 B9Y55_RS11060 galactose/methyl galactoside ABC transporter permease MglC
Query= TCDB::Q9WXW7 (317 letters) >NCBI__GCF_900177735.1:WP_085545417.1 Length = 329 Score = 177 bits (450), Expect = 2e-49 Identities = 116/318 (36%), Positives = 171/318 (53%), Gaps = 20/318 (6%) Query: 17 VALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMVA 76 V L L V A ++PRFL+ L+ + Q + +LA+G F++I+GG +DLS G MV Sbjct: 15 VVLAFLIVVIATIDPRFLSLAILRDILMQSSTRAILALGVAFILITGG--VDLSSGRMVG 72 Query: 77 LTGVMVAWLMTHGVPV--------WISVILILLFSIGA----GAWHGLFVTKLRVPAFII 124 V+ A ++ + V ISVI +L +I A G +G+ V KL VP FI Sbjct: 73 FAAVISASMLQNADYVRRFYPDMAQISVIFPILLAIAACMILGMLNGVIVAKLNVPPFIT 132 Query: 125 TLGTLTIARGMAAVI-----TKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADF 179 TLG + + G+ ++ PI G+ F G G IP+ + I LAVA++ Sbjct: 133 TLGMMVVVYGINSIYFDMPPNNSQPIGGIRPDFTWFGSGYAGGIPVIILIALAVAILVWV 192 Query: 180 FLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPG 239 KT+ G ++ A GGN AA SG+NV + ++ + ++G L GV G + AAR Sbjct: 193 LFNKTLLGMNMYAIGGNREAAEVSGINVVKTLILLYAIAGALYGVAGFLEAARTGGATNN 252 Query: 240 VGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGI 299 G+MYEL AIAS V+GG S TGG G+V G + G I ++ L + V+ YW ++ G+ Sbjct: 253 YGTMYELDAIASCVVGGVSTTGGVGTVPGVLAGVLIFGVINYGLTFIGVNPYWQLIIKGL 312 Query: 300 VIVVAVTLDILRRRLASK 317 +IV AV DI R+ +A K Sbjct: 313 IIVAAVAFDI-RKYVAKK 329 Lambda K H 0.328 0.143 0.424 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: 321 Number of extensions: 21 Number of successful extensions: 3 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: 317 Length of database: 329 Length adjustment: 28 Effective length of query: 289 Effective length of database: 301 Effective search space: 86989 Effective search space used: 86989 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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