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 GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 273 bits (697), Expect = 1e-77 Identities = 155/344 (45%), Positives = 213/344 (61%), Gaps = 26/344 (7%) Query: 26 LMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVA-GLTIMVPILGG 84 L+TGVSFM+P V GG+ +A+++ G F+ G+ L QIG +M+P+L G Sbjct: 252 LLTGVSFMLPMVVAGGLLIALSFVFGIE--AFQEEGTLAAALMQIGGGTAFKLMIPLLAG 309 Query: 85 YIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAGYVA 144 YIA++IADRPGLAPG + ++ GE GAG+LG IVAG LAGYVA Sbjct: 310 YIAWSIADRPGLAPGMIGGFL-----------------AGELGAGFLGGIVAGFLAGYVA 352 Query: 145 RFF-KNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQGGQ 203 RF + L +PE I+ + P+L+IP+ V M++V+G P+A LT FL+ M Sbjct: 353 RFISQKLPMPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTN 412 Query: 204 AIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEI--YAPMAAVMIGGMIPPIGLALSN 261 AI++G ILG MM FD+GGPVNK AY F GL++E APMAA+M GM+P IG+ +++ Sbjct: 413 AILLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVAS 472 Query: 262 FIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMALG 321 FIA K+A + G++ VLGL FI+EGAIP+ A DPLRVIP + G A+ GA SM Sbjct: 473 FIARRKFAEAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLFT 532 Query: 322 VTMPAPHGGIFVVLLSN---QPLAFLGSILLGSLVTAVVATVIK 362 V + APHGG+FV+ + N L +L +I +GSLV ++K Sbjct: 533 VKLMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLK 576 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: 841 Number of extensions: 47 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: 383 Length of database: 587 Length adjustment: 33 Effective length of query: 350 Effective length of database: 554 Effective search space: 193900 Effective search space used: 193900 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