GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-C in Escherichia coli BW25113

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)



>lcl|FitnessBrowser__Keio:16276 b2167 fused fructose-specific PTS
           enzymes: IIBcomponent/IIC components (NCBI)
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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