Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate AZOBR_RS32335 AZOBR_RS32335 PTS fructose transporter subunit IIBC
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__azobra:AZOBR_RS32335 Length = 580 Score = 294 bits (753), Expect = 4e-84 Identities = 160/344 (46%), Positives = 223/344 (64%), Gaps = 25/344 (7%) Query: 26 LMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENT--GSAGWFLAQIGVAG-LTIMVPIL 82 LMTGVSFM+PFV GG+ +A+A+A+G VFE++ G+ G L QIG G +MVP L Sbjct: 246 LMTGVSFMLPFVVTGGLLIAIAFALGGIY-VFEDSQQGTLGNALFQIGAKGAFALMVPAL 304 Query: 83 GGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAGY 142 GYIA++IADRPG+ PG V GI GAG+LG IVAG +AGY Sbjct: 305 AGYIAFSIADRPGITPGM-----------------VGGILAANLGAGFLGGIVAGFIAGY 347 Query: 143 VARFF-KNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQG 201 F +N+ + + ++ + PVL++P+ V M++V+G PVA A L+++L+ MQG Sbjct: 348 ATSFLNRNIRLHKNLEGLKPVLILPLLGSLVTGLAMIYVVGAPVAEALATLSAWLKGMQG 407 Query: 202 GQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMIGGMIPPIGLALSN 261 AI++GL++G MMAFDMGGPVNK AY F+TGLI ++Y PMAA M GM+PP+GLAL+ Sbjct: 408 SSAILLGLLIGAMMAFDMGGPVNKAAYAFSTGLIASQVYTPMAAAMAAGMVPPLGLALAT 467 Query: 262 FIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMALG 321 + ++ E E G + +LG++FITEGAIP+AA DPLRVIPA+V G+A+ GA SM +G Sbjct: 468 KLFADRFTREEREAGNAAGILGIAFITEGAIPFAARDPLRVIPALVLGAALTGAISMGIG 527 Query: 322 VTMPAPHGGIFVVLLSNQPLAFLG---SILLGSLVTAVVATVIK 362 + PHGGIFV+ + N G +++ G++ TAV +K Sbjct: 528 AELKVPHGGIFVLPIPNAVTHLAGYVVALVAGTVTTAVALRFLK 571 Lambda K H 0.322 0.139 0.399 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: 782 Number of extensions: 52 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: 383 Length of database: 580 Length adjustment: 33 Effective length of query: 350 Effective length of database: 547 Effective search space: 191450 Effective search space used: 191450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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