GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Pseudomonas simiae WCS417

Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate GFF5410 PS417_27695 alanine racemase

Query= SwissProt::Q88GJ9
         (409 letters)



>FitnessBrowser__WCS417:GFF5410
          Length = 357

 Score =  112 bits (280), Expect = 2e-29
 Identities = 113/361 (31%), Positives = 166/361 (45%), Gaps = 28/361 (7%)

Query: 48  VSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEAR 107
           +   AL+HN + L  E+ G +K  AV+KADAYGHG   V  ++ A+     AVA  EEA 
Sbjct: 8   IDLQALRHNYQ-LAREVTG-AKALAVIKADAYGHGAVRVAQALQAEA-DGFAVACIEEAL 64

Query: 108 VVRASGFTGQLVRVR-LASLSELEDGLQYDMEELVGSAEFARQADAIA-ARHGKTLRIHM 165
            +RA+G    ++ +       EL   +++D   +V S     Q +AI  A+  K L I +
Sbjct: 65  ELRAAGIRAPVLLLEGFFEADELPLIIEHDFWCVVHSLW---QLEAIEQAKLSKPLTIWL 121

Query: 166 ALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDKDDVRKG---LAAFN 222
            L+S GM R G+    +    + L +   K  K+V LM+HFA  D+ D  +    +A F+
Sbjct: 122 KLDS-GMHRVGLHPKDYHEAYQRL-LASGKVAKIV-LMSHFARADELDCVRSDEQVAVFD 178

Query: 223 EQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGAL-----FGDTVPARTEY 277
                L     L          NS + +  P    D VR G  L     FG+     +  
Sbjct: 179 AARQGLSAEVSL---------RNSPSVIGWPNVSSDWVRPGIMLYGATPFGEDQAIASRL 229

Query: 278 KRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLIN 337
           +  M  +S V  V   PAG  VGY   F   +  R+  + +GY+DGY R       VL+ 
Sbjct: 230 QPVMTLESKVICVRELPAGEPVGYGAKFITPKPMRIGVVAMGYADGYPRHAPTGTPVLVA 289

Query: 338 GHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQAGGEITQAEMEEINGALLADLYT 397
           G R  ++G+VSM+ L +D+TD P    G+ V L+GK           E I   L  +L  
Sbjct: 290 GQRSQLLGRVSMDMLCIDLTDLPQAGLGSTVELWGKNILASDVAVAAETIPYQLFCNLRR 349

Query: 398 V 398
           V
Sbjct: 350 V 350


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: 323
Number of extensions: 15
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: 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.

Links

Downloads

Related tools

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