GapMind for catabolism of small carbon sources

 

Aligments for a candidate for orr in Phaeobacter inhibens BS107

Align Lysine racemase; Lys racemase; Ornithine racemase; EC 5.1.1.5; EC 5.1.1.12 (characterized)
to candidate GFF1737 PGA1_c17610 putative alanine racemase

Query= SwissProt::Q9X1T3
         (354 letters)



>lcl|FitnessBrowser__Phaeo:GFF1737 PGA1_c17610 putative alanine
           racemase
          Length = 373

 Score =  172 bits (436), Expect = 1e-47
 Identities = 122/353 (34%), Positives = 185/353 (52%), Gaps = 7/353 (1%)

Query: 1   MVYPRLLINLKEIEENARKVVEMASRRGIEIVGVTKVTLGDPRFAETLRKAGIGILGESR 60
           M  PR+ I+L +I +N R +VE     GI + GVTK   G P  A  +   G   L ++R
Sbjct: 1   MTAPRIKIDLHKIRDNTRCLVERLKPLGITVTGVTKGVCGHPGVARAMLDGGAIGLADAR 60

Query: 61  IRNVLRMKKAGIEGPFMLLRLPMMSELVEDVKHFDYIMVSDPDVAKKVDELSREMKRNVK 120
           + NV RM+KAG+  P +++R PM+S+  + V+  +    ++  V  K+   +     + +
Sbjct: 61  LANVRRMRKAGLTCPILMIRTPMLSQAGQIVETCEASCNTETSVIAKLAAAALRRGISHE 120

Query: 121 IIYMIDVGDLREGVWFE---KAVEEIAQCRGANIVGIGTNFGCYGGIIPTREKFEILLDI 177
           II M+++GD REG+  E    A   + +  G  + GIG NFGC     PT +   +L  +
Sbjct: 121 IILMVEMGDGREGIMPEDLTNAALHVTRTPGVLLKGIGANFGCLADAAPTSQAMAVLSSL 180

Query: 178 KEKLEKNHGFNIEIVSGGNTPALYALENGEIPEGINQLRIGEAIVLGRDITNNRVIDWLS 237
            ++ E   G  +E VSGG++  L    +G   + IN LRIGEAI+LG D  +   I  L 
Sbjct: 181 ADETEGACGPFVETVSGGSSANLSWALDGGPADRINNLRIGEAILLGTDPVSGHPISGLY 240

Query: 238 QNTFLIEAEVIEVKEKPSVPLGKRGLDVFGRKVDFV-DRGIRKRAICALGEQDIDSRGLI 296
            + F + AEVIE K K S P+  +  D     +  V       R+I ALG QD D+ GL 
Sbjct: 241 TDAFTLLAEVIETKIK-SKPVPLKLSDPALSALSLVPGNHWTTRSILALGLQDTDAAGL- 298

Query: 297 PVDKGVEVLHASSDHIVLDVTDFGDVKVGDVFRFRMTYSCLLKAMTSPFVEKV 349
                V    A+SDHIV++ T+   +++G     +M+YS L +AM +P V KV
Sbjct: 299 TFPAAVIFAGATSDHIVVETTNC-PLRIGSEMSMKMSYSALARAMEAPDVSKV 350


Lambda     K      H
   0.321    0.142    0.407 

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: 289
Number of extensions: 14
Number of successful extensions: 4
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: 354
Length of database: 373
Length adjustment: 29
Effective length of query: 325
Effective length of database: 344
Effective search space:   111800
Effective search space used:   111800
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: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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