GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Pseudomonas fluorescens FW300-N2E2

Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate Pf6N2E2_4393 Alanine racemase (EC 5.1.1.1)

Query= SwissProt::Q88GJ9
         (409 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4393
          Length = 357

 Score =  120 bits (300), Expect = 8e-32
 Identities = 107/335 (31%), Positives = 157/335 (46%), Gaps = 26/335 (7%)

Query: 48  VSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEAR 107
           +   AL+HN + L  E+ G +K  AV+KADAYGHG  +     +       AVA  EEA 
Sbjct: 8   IDLQALRHNYQ-LAREVTG-AKALAVIKADAYGHG-AVRCAEALQDTADGFAVACIEEAL 64

Query: 108 VVRASGFTGQLVRVR-LASLSELEDGLQYDMEELVGSAEFARQADAIAARHGKTLRIHMA 166
            +RA G  G ++ +      SEL   +++D   +V S       +  A     T+ + + 
Sbjct: 65  ELRAGGIRGPILLLEGFFEASELSLIVEHDFWCVVHSLWQLEAIEKAALSQPITVWLKL- 123

Query: 167 LNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDK---DDVRKGLAAFNE 223
              SGM R G+  A +      L +   K  K+V LM+HFA  D+       + LA F++
Sbjct: 124 --DSGMHRVGLHPADYQAAYRRL-LASGKVAKIV-LMSHFARADELHDPSSTEQLAIFDK 179

Query: 224 QTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDTV-----PARTEYK 278
               L+    L          NS A L  P+   D VR G  L+G T         +  +
Sbjct: 180 ARQGLVAQISL---------RNSPAVLGWPQVPSDWVRPGIMLYGATPFDEPNAVASRLQ 230

Query: 279 RAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLING 338
             M  +S +  V   PAG  VGY   F   + +R+  + +GY+DGY R   N   VL++G
Sbjct: 231 PVMTLESKIICVRELPAGEPVGYGARFVTTQPTRVGVVAMGYADGYPRQAPNGTPVLVDG 290

Query: 339 HRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGK 373
            R  +VG+VSM+ L VD+TD P    G+ V L+GK
Sbjct: 291 QRSQLVGRVSMDMLCVDLTDVPQAGLGSTVELWGK 325


Lambda     K      H
   0.318    0.132    0.377 

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: 324
Number of extensions: 8
Number of successful extensions: 3
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: 409
Length of database: 357
Length adjustment: 30
Effective length of query: 379
Effective length of database: 327
Effective search space:   123933
Effective search space used:   123933
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 (21.7 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