GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr 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)



>FitnessBrowser__Phaeo:GFF1737
          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 (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