GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-C in Pseudomonas putida KT2440

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 PP_0795 PP_0795 fructose PTS permease - IIBC component

Query= TCDB::Q5V5X5
         (383 letters)



>lcl|FitnessBrowser__Putida:PP_0795 PP_0795 fructose PTS permease -
           IIBC component
          Length = 580

 Score =  299 bits (765), Expect = 2e-85
 Identities = 166/361 (45%), Positives = 225/361 (62%), Gaps = 24/361 (6%)

Query: 7   DQNRAESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWF 66
           D   A +  ++  T V + L+TGVSFM+P V  GG+ +A+++  G     ++  G+    
Sbjct: 224 DAAAATTPTKSEKTGVYKHLLTGVSFMLPMVVAGGLLIALSFVFGIE--AYKEAGTLPAA 281

Query: 67  LAQIG-VAGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGE 125
           L QIG  A   +MVP+L GYIA++IADRPGLAPG                  + G+    
Sbjct: 282 LMQIGGEAAFKLMVPLLAGYIAWSIADRPGLAPGM-----------------IGGLLAST 324

Query: 126 AGAGYLGAIVAGLLAGYVARFFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVP 184
            GAG++G IVAG LAGY A+       +P  ++ + P+L+IP+        +M++V+G P
Sbjct: 325 LGAGFIGGIVAGFLAGYSAKAIARWARLPSSLEALKPILIIPLLASLFTGLVMIYVVGQP 384

Query: 185 VALANEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMA 244
           VA   EGLT FL SM    AI++GL+LGGMM  D+GGP+NK AY F+ GL+    YAPMA
Sbjct: 385 VAAMLEGLTHFLDSMGTTNAILLGLLLGGMMCVDLGGPINKAAYAFSVGLLASSSYAPMA 444

Query: 245 AVMIGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIP 304
           A M  GM+PPIGL ++ F+A  K+A    E GK+ + LGL FI+EGAIP+AA DPLRVIP
Sbjct: 445 ATMAAGMVPPIGLGIATFLARRKFAQSEREAGKAALALGLCFISEGAIPFAAKDPLRVIP 504

Query: 305 AIVAGSAVGGATSMALGVTMPAPHGGIFVVLLS---NQPLAFLGSILLGSLVTAVVATVI 361
           A +AG A+ GA SM  G  + APHGG+FV+L+    N  L +L +I+ GSLVTAVV  VI
Sbjct: 505 ASIAGGALTGALSMYFGCKLMAPHGGLFVLLIPNAINHALLYLLAIVAGSLVTAVVYAVI 564

Query: 362 K 362
           K
Sbjct: 565 K 565


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: 750
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: 580
Length adjustment: 33
Effective length of query: 350
Effective length of database: 547
Effective search space:   191450
Effective search space used:   191450
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 preprint 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