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 WP_013404311.1 CALHY_RS12545 PTS transporter subunit EIIC
Query= TCDB::Q5V5X5 (383 letters) >NCBI__GCF_000166355.1:WP_013404311.1 Length = 454 Score = 290 bits (741), Expect = 7e-83 Identities = 165/359 (45%), Positives = 227/359 (63%), Gaps = 25/359 (6%) Query: 11 AESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQI 70 A+ + T V + LMTGVS+MIPFV GGI +A+++A G FE G+ L I Sbjct: 112 AKKEAKEKATGVYKHLMTGVSYMIPFVVAGGILIAISFAFGIK--AFEKKGTLAAALMDI 169 Query: 71 GV-AGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAG 129 G + +MVPIL G+IA++IADRPGL PG + G+ + GAG Sbjct: 170 GGGSAFYLMVPILAGFIAFSIADRPGLVPGM-----------------IGGLLANKLGAG 212 Query: 130 YLGAIVAGLLAGY-VARFFKNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALA 188 +LG IVAG AGY VA K + +P+ ++ +MPVL++PV + ++ M++V+G PVA Sbjct: 213 FLGGIVAGFAAGYLVAWLKKTIKLPKTMEGLMPVLILPVLSTLIIGLGMIYVVGEPVAAL 272 Query: 189 NEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATG-LITEEIYAPMAAVM 247 N+ +T +L+SM G A+++G+ILG MMAFDMGGPVNK AY FA L + MAAVM Sbjct: 273 NKAMTEWLKSMSSGSAVLLGIILGLMMAFDMGGPVNKAAYTFAVSTLAAGQPSTIMAAVM 332 Query: 248 IGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIV 307 GM PP+GLAL+ IA K+ E E GK+ LG+SFITEGAIP+AAADPLRVIP+I+ Sbjct: 333 AAGMTPPLGLALATLIAKDKFTTEEREAGKAAFFLGISFITEGAIPFAAADPLRVIPSIM 392 Query: 308 AGSAVGGATSMALGVTMPAPHGGIFVVLLSN---QPLAFLGSILLGSLVTAVVATVIKP 363 GSAV S+ T+ PHGGIFV+ + N L + +I +G++VTA++ +V+KP Sbjct: 393 IGSAVTSTLSILFKCTLAVPHGGIFVLPIPNAVGNLLLYAVAIAIGTVVTALIVSVLKP 451 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: 621 Number of extensions: 45 Number of successful extensions: 7 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: 454 Length adjustment: 31 Effective length of query: 352 Effective length of database: 423 Effective search space: 148896 Effective search space used: 148896 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: 50 (23.9 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