GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Escherichia coli BW25113

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)

Query= TCDB::P71012
         (635 letters)



>FitnessBrowser__Keio:16276
          Length = 563

 Score =  404 bits (1039), Expect = e-117
 Identities = 211/473 (44%), Positives = 308/473 (65%), Gaps = 17/473 (3%)

Query: 162 AAPAPAGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQE 221
           A  A +G  +++AVTACPTG+AHTFMAA+A++ +AK+ G  +KVET GS G  + +T +E
Sbjct: 96  APVAASGPKRVVAVTACPTGVAHTFMAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEE 155

Query: 222 IEDAPAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSA 281
           +  A  +IVAAD +V++ +F GK + +      +++  + ++KA+ +  P Y+ +G    
Sbjct: 156 VAAADLVIVAADIEVDLAKFAGKPMYRTSTGLALKKTAQELDKAVAEATP-YEPAGKAQT 214

Query: 282 ASNDDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSY 341
           A+   E  K  +G+      Y+HL++GVS MLP VV GG+ +A+SF +GI +    +P  
Sbjct: 215 ATT--ESKKESAGA------YRHLLTGVSYMLPMVVAGGLCIALSFAFGIEAF--KEPG- 263

Query: 342 NTFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIA 401
            T AAAL  IGG +A  L+V VLAG+IA SIADRPG  PG++GG +A    +GF+GG+IA
Sbjct: 264 -TLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLTPGLIGGMLAVSTGSGFIGGIIA 322

Query: 402 GFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTN 461
           GFLAGY+  L+      +PQS++ LKP+LI PL    + G+ M +++  PVA  +  LT+
Sbjct: 323 GFLAGYIAKLISTQLK-LPQSMEALKPILIIPLISSLVVGLAMIYLIGKPVAGILEGLTH 381

Query: 462 WLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPP 521
           WL+++GT N VL+G ILGGMM  DMGGP+NKAA+ FG+ ++    Y P AAIMA GMVPP
Sbjct: 382 WLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYGPMAAIMAAGMVPP 441

Query: 522 LGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAG 581
           L + LAT + R KF +  +E G     +G  F++EGAIPFAA DP+RV+P  +VG A+ G
Sbjct: 442 LAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIPFAARDPMRVLPCCIVGGALTG 501

Query: 582 GLTEFFRVTLPAPHGGVFVAFITN--HPML-YLLSIVIGAVVMAIILGIVKKP 631
            ++      L APHGG+FV  I     P+L YL++I+ G +V  +    +K+P
Sbjct: 502 AISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAGTLVAGLAYAFLKRP 554


Lambda     K      H
   0.320    0.137    0.390 

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: 831
Number of extensions: 42
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: 635
Length of database: 563
Length adjustment: 37
Effective length of query: 598
Effective length of database: 526
Effective search space:   314548
Effective search space used:   314548
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 (21.8 bits)
S2: 53 (25.0 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:

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