GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N2C3

Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate AO356_00950 AO356_00950 ribokinase

Query= SwissProt::D4GYE6
         (305 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00950
          Length = 304

 Score = 86.7 bits (213), Expect = 6e-22
 Identities = 85/273 (31%), Positives = 120/273 (43%), Gaps = 31/273 (11%)

Query: 37  GGKGINVAKYASALDADVTASGFLGGH-FGKFVRDRLDADGIASDFVTVDADTRLNTTVL 95
           GGKG N A  A+ L A V+  G +G   +G+ +R  L A+GI    V V+  +     ++
Sbjct: 39  GGKGANQAVAAARLGAQVSMVGCVGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIV 98

Query: 96  AADGEYKL-----NHNGPQIRAA--DVDELVETA-----QANEPDTLLVGGSLPPGMSLS 143
             D            NG         VD+++++A     Q   PD   VG +L  G +L 
Sbjct: 99  VDDNSQNAIVIVAGANGALTAEVLDGVDDVLQSADVIICQLEVPDAT-VGHALKRGRALG 157

Query: 144 DVDRLARAGDWKIAVDMGGEYLAELDADYYVCK----PNRSELAAATGRTVETEADAVEA 199
                      KI +         L AD+Y C     PN SE A  +G  V++   A  A
Sbjct: 158 -----------KIVILNPAPASHALPADWYACIDYLIPNESEAAVLSGLAVDSLETAEAA 206

Query: 200 AEELHARGFEYVLASLGADGALLVTDDEVLSAPALDVEVVDTVGAGDAVMSGFLAAREHG 259
           A  L A G   V+ +LGA G +          PA  V+ VDT  AGD  + GF AA   G
Sbjct: 207 AAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPAPRVKAVDTTAAGDTFVGGFAAALACG 266

Query: 260 LSDADALRMGVLTASRVVGVAGTR--VPDLEDV 290
            S+ DA+R G + A+  V  AG +  +P L +V
Sbjct: 267 KSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEV 299


Lambda     K      H
   0.315    0.133    0.375 

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: 224
Number of extensions: 23
Number of successful extensions: 2
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: 305
Length of database: 304
Length adjustment: 27
Effective length of query: 278
Effective length of database: 277
Effective search space:    77006
Effective search space used:    77006
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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