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 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__Keio:16276 Length = 563 Score = 282 bits (722), Expect = 1e-80 Identities = 154/375 (41%), Positives = 230/375 (61%), Gaps = 30/375 (8%) Query: 4 TMTDQNRAESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSA 63 T T +++ ESA L+TGVS+M+P V GG+ +A+++A G F+ G+ Sbjct: 214 TATTESKKESA------GAYRHLLTGVSYMLPMVVAGGLCIALSFAFGIE--AFKEPGTL 265 Query: 64 GWFLAQIGV-AGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGIS 122 L QIG + +MVP+L GYIA++IADRPGL PG + G ++A + Sbjct: 266 AAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLTPGLI-------GGMLAVST------ 312 Query: 123 GGEAGAGYLGAIVAGLLAGYVARFFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVL 181 G+G++G I+AG LAGY+A+ L +P+ ++ + P+L+IP+ + V+ M++++ Sbjct: 313 ----GSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVVGLAMIYLI 368 Query: 182 GVPVALANEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYA 241 G PVA EGLT +LQ+M A+++G ILGGMM DMGGPVNK AY F GL++ + Y Sbjct: 369 GKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYG 428 Query: 242 PMAAVMIGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLR 301 PMAA+M GM+PP+ + L+ +A K+ E GK+ +VLGL FI+EGAIP+AA DP+R Sbjct: 429 PMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIPFAARDPMR 488 Query: 302 VIPAIVAGSAVGGATSMALGVTMPAPHGGIFVVLLS---NQPLAFLGSILLGSLVTAVVA 358 V+P + G A+ GA SMA+G + APHGG+FV+L+ L +L +I+ G+LV + Sbjct: 489 VLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAGTLVAGLAY 548 Query: 359 TVIKPDFEDRVDTGA 373 +K D V A Sbjct: 549 AFLKRPEVDAVAKAA 563 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: 48 Number of successful extensions: 6 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: 563 Length adjustment: 33 Effective length of query: 350 Effective length of database: 530 Effective search space: 185500 Effective search space used: 185500 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