GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudomonas fluorescens GW456-L13

Align Fructokinase; EC 2.7.1.4 (characterized)
to candidate PfGW456L13_3908 Ribokinase (EC 2.7.1.15)

Query= SwissProt::P26420
         (307 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908
          Length = 305

 Score = 85.5 bits (210), Expect = 1e-21
 Identities = 93/323 (28%), Positives = 134/323 (41%), Gaps = 42/323 (13%)

Query: 1   MNGKIWVLGDAVVDL------LPDGEGRLL-----QCPGGAPANVAVGVARLGGDSGFIG 49
           M+ K+ V+G   +DL      LP G   L+        GG  AN AV  ARLG     IG
Sbjct: 1   MSAKVVVIGSLNMDLVTRAPRLPKGGETLIGQSFTTVSGGKGANQAVAAARLGAQVSMIG 60

Query: 50  RVGDDPFGRFMRHTLAQEQVDVNYMR-LDAAQRTSTVVVDLDSHGERTFTFMVRPSADLF 108
            VG+D +G  +R  L  EQ+D   +  +D +   + +VVD  S      + ++ P A+  
Sbjct: 61  CVGNDAYGEALRGALLAEQIDCRAVSTVDGSSGVALIVVDDSSQN----SIVIVPGANGA 116

Query: 109 LQPEDLPPFAA---GQWLHVCSIALSAEPSRSTTFAALEAIKRAGGYVSFDPNIRSDLWQ 165
           L  E +  F +      + +C +    E   ++   AL+  +  G  V  +P   S    
Sbjct: 117 LTAETIDRFDSVIRAADVLICQL----EVPDASVGHALKRGRELGKTVILNPAPAS---- 168

Query: 166 DPQDLRDCLDRALALADAIKLSEEELAFISG----SDDIVSGIARLNARFQPTLLLVTQG 221
                R       A  D +  +E E + +SG    S D     A          +++T G
Sbjct: 169 -----RPLPSDWYASIDYLIPNESEASALSGLSVDSLDTAQAAATRLIALGAGKVIITLG 223

Query: 222 KAGVQAALRGQVSHFPARPVVAVDTTGAGDAFVAGLLAGLAAHGIPDNLAALAPDLALAQ 281
             G   A   +  HFPA  V AVDTT AGD FV G  A LAA          A  +   Q
Sbjct: 224 AQGSLFADGQRFEHFPAPVVKAVDTTAAGDTFVGGFAAALAAGNDE------AQAIRFGQ 277

Query: 282 TCGALATTAKGAMTALPYKDDLQ 304
              AL+ T  GA  ++P   D+Q
Sbjct: 278 VAAALSVTRAGAQPSIPALSDVQ 300


Lambda     K      H
   0.321    0.137    0.406 

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: 190
Number of extensions: 8
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: 307
Length of database: 305
Length adjustment: 27
Effective length of query: 280
Effective length of database: 278
Effective search space:    77840
Effective search space used:    77840
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: 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