Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate BWI76_RS27885 BWI76_RS27885 PTS alpha-glucoside transporter subunit IICB
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__Koxy:BWI76_RS27885 Length = 540 Score = 181 bits (459), Expect = 5e-50 Identities = 137/440 (31%), Positives = 208/440 (47%), Gaps = 41/440 (9%) Query: 1 MAVLQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEF--------PAFVTKIAGFMAAG 52 ++ +QR G ++ PV + P A ++V G A ML P F + +I + G Sbjct: 2 LSQIQRFGGAMFTPVLLFPFAGIVV--GIAIMLRNPMFVGEALTAPDSLFAQIVHIIEEG 59 Query: 53 GNAILDNMALLFAVGIAIGFAKKSDGSTALAAVVGYLV---FKNVLAT----FTDKNLPQ 105 G + NM L+FAVG+ IG AK++ G LA +V +L F N + F + Sbjct: 60 GWTVFRNMPLIFAVGLPIGLAKQAQGRACLAVLVSFLTWNYFINAMGMTWGHFFGVDFSV 119 Query: 106 VAKAVDGKVVMVDAP-VDAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILS 164 A G +M +D ++G +V+ +V L+ R++ LP + G F G V I++ Sbjct: 120 EPTAGSGLTMMAGIKTLDTSIIGAIVISGLVTALHNRYFDKPLPVFLGIFQGSSFVVIVA 179 Query: 165 AFAGLVIGIVFGYIWPVLGTGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFP 224 A + + WP + G+ + +L +GA+G ++ R LIP G+HH + Sbjct: 180 FLAMIPCAWLTLLGWPKVQMGIESLQAFLRSAGALGVWVYIFLERILIPTGLHHFVYGPF 239 Query: 225 WFQAGEYEGKSGDI-ARFLAGDPTAGQFMTGFFPIMMFALPA---------ACLAIVHCA 274 F EG A+ L + + + FP FAL LA+ A Sbjct: 240 IFGPAVVEGGIQVYWAQHLQAFSQSTEALKTLFPEGGFALHGNSKVFGSVGIALALYFTA 299 Query: 275 RPERRKVVGGMMFSLALTSFVTGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMK 334 PE R V G++ LT+ + G+TEP+EFTF+FI+P+L+A+HAVL + + G+ Sbjct: 300 APENRVKVAGLLIPATLTAMLVGITEPLEFTFLFISPLLFAVHAVLAATMATVMYICGVV 359 Query: 335 DGFGFSAGAVDFFLNL-------GIASNPWGLALVGVCFAALYYVVFRFAITKFNLPTPG 387 FG G +D FL AS + VGVCF ALY+V+FR I + NL TPG Sbjct: 360 GNFG--GGLLDQFLPQNWIPMFHNHASMMFIQIGVGVCFTALYFVIFRTLILRLNLKTPG 417 Query: 388 RESDE----ELAELRKAEGK 403 RE E A+ + A GK Sbjct: 418 REESEIKLYSKADYQAARGK 437 Lambda K H 0.328 0.143 0.441 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: 612 Number of extensions: 42 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: 403 Length of database: 540 Length adjustment: 33 Effective length of query: 370 Effective length of database: 507 Effective search space: 187590 Effective search space used: 187590 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: 51 (24.3 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