GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Pseudomonas fluorescens FW300-N1B4

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate Pf1N1B4_398 Galactonate dehydratase (EC 4.2.1.6)

Query= BRENDA::A9CEQ8
         (378 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_398
          Length = 382

 Score =  171 bits (432), Expect = 4e-47
 Identities = 125/357 (35%), Positives = 181/357 (50%), Gaps = 33/357 (9%)

Query: 34  VEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQR 91
           +++E D+G  GWGE +  G A   AA V+  S +LIG+DPR  E IW VLY     +G  
Sbjct: 18  LKVETDEGVTGWGEPVVEGRAHTVAAAVEELSDYLIGKDPRNIEDIWTVLYRGGFYRGG- 76

Query: 92  GLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNASE 151
            + ++AL+GID ALWDIKGK  G S+S LLGG+ R+ +R Y+         DR +D A  
Sbjct: 77  AIHMSALAGIDQALWDIKGKALGVSVSDLLGGQVRDKIRVYSW-----IGGDRPADTARA 131

Query: 152 MAERRAEGFHACKIKIGFGVEE----------DLRV--IAAVREAIGPDMRLMIDANHGY 199
             E  + GF A K+    G EE          DL +  +AAVR+A+GP++ + +D +   
Sbjct: 132 AKEAVSRGFTAVKMN---GTEELQFLDSFEKVDLALANVAAVRDAVGPNVGIGVDFHGRV 188

Query: 200 TVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQALS 259
               A  L      + + + EEPV+ E  +A   +      P+A GE    R+   + LS
Sbjct: 189 HKPMAKVLMKELDPYKLMFIEEPVLSENYEALKELAPLTSTPIALGERLFSRWDFKRVLS 248

Query: 260 AGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPV 319
            G VDI+QPD    GG +E +KIA +A  + V +  H     + +AA LQ       D V
Sbjct: 249 EGYVDIIQPDASHAGGITETRKIANMAEAYDVALALHCPLGPIALAACLQL------DAV 302

Query: 320 RVNPIEPIMEFDRTHNPFRQAV--LREP--LEAVNGVVTIPDGPGLGIEINRDALTE 372
             N           +N     +  +++P   +   G V IP+GPGLGIEIN + + E
Sbjct: 303 CYNAFIQEQSLGIHYNESNDLLDYVKDPRVFDYDKGFVKIPNGPGLGIEINEEYVIE 359


Lambda     K      H
   0.321    0.138    0.431 

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: 427
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 378
Length of database: 382
Length adjustment: 30
Effective length of query: 348
Effective length of database: 352
Effective search space:   122496
Effective search space used:   122496
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: 50 (23.9 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