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_110805521.1 C8J30_RS09070 PTS fructose-like transporter subunit IIB
Query= TCDB::Q5V5X5 (383 letters) >NCBI__GCF_003217355.1:WP_110805521.1 Length = 578 Score = 298 bits (762), Expect = 3e-85 Identities = 163/342 (47%), Positives = 225/342 (65%), Gaps = 24/342 (7%) Query: 26 LMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVAGLTIMVPILGGY 85 L+TGVS+M+P V GG+ +A+++ G E T A +A G A +MVP+L G+ Sbjct: 245 LLTGVSYMLPLVVAGGLLIALSFVFGIKAFEVEGTLPAA-LMAIGGGAAFKLMVPVLAGF 303 Query: 86 IAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAGYVAR 145 IAY+IADRPGL PG + G ++A AG+LG IVAG LAGYVAR Sbjct: 304 IAYSIADRPGLTPGLI-------GGMLAV----------NLNAGFLGGIVAGFLAGYVAR 346 Query: 146 FFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQGGQA 204 + ++ + +P ++ + PVL++P+ + A+ +M++++G PVA +T+FLQ + A Sbjct: 347 WLRDAIQLPRTLEGLKPVLILPLLSTAITGLVMVYIVGTPVAALLAAMTAFLQGLGTTNA 406 Query: 205 IVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMIGGMIPPIGLALSNFIA 264 +V+GLILGGMMA DMGGP+NK AY FA GL+T YAPMAAVM GM PP+GLAL+ +A Sbjct: 407 VVLGLILGGMMAVDMGGPINKAAYTFAVGLLTSNTYAPMAAVMAAGMTPPLGLALATLVA 466 Query: 265 PHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMALGVTM 324 +++ AE E G + VLGLSFITEGAIP+AA DP RVIP+I+ GSA+ GA SMALG + Sbjct: 467 KNRFTAEEREAGGAAAVLGLSFITEGAIPFAAKDPARVIPSIIVGSAITGALSMALGCLL 526 Query: 325 PAPHGGIFVVLLSNQPLAFLG----SILLGSLVTAVVATVIK 362 APHGGIFV+ + N + LG SI++G+LVT + +K Sbjct: 527 VAPHGGIFVLAIPN-AVTNLGLYALSIVVGTLVTTGLLIALK 567 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: 767 Number of extensions: 39 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: 578 Length adjustment: 33 Effective length of query: 350 Effective length of database: 545 Effective search space: 190750 Effective search space used: 190750 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 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