GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Pseudomonas litoralis 2SM5

Align (S)-2-hydroxyglutarate oxidase (characterized)
to candidate WP_090274570.1 BLU11_RS14525 NAD(P)/FAD-dependent oxidoreductase

Query= metacyc::G1G01-3089-MONOMER
         (416 letters)



>NCBI__GCF_900105005.1:WP_090274570.1
          Length = 370

 Score =  143 bits (360), Expect = 1e-38
 Identities = 110/394 (27%), Positives = 178/394 (45%), Gaps = 51/394 (12%)

Query: 3   DFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGSLK 62
           + I++G G+VG++ A  L     D  +++LE+E+    H +  NS VIHAG+YY  GSLK
Sbjct: 5   EVIVVGAGVVGLAIAQRLASGGRD--VMILEREASIGEHASSRNSEVIHAGIYYPSGSLK 62

Query: 63  ARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLSAD 122
           AR CL+G     A+C  H +     GKLLVAT D E+  ++ L     A G++   L+A 
Sbjct: 63  ARLCLDGRDRLYAWCEAHRVPHRRIGKLLVATADDELPALEQLRFNAQACGVQLQSLNAA 122

Query: 123 ELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANEVI 182
           ++ E EP +  +GG+F P +GIV+   +  +        GG++     V  ++ Q    +
Sbjct: 123 QVHELEPAVTAVGGLFSPLTGIVDSHALMQSFETVLLGQGGQLCLRTRVDRVERQGERWL 182

Query: 183 VRTQRD----ELHSRFLVTCSGLMADRVVGMLGLRTEFVICPF---RGEYYLLPKQHNQI 235
           V+ Q       +  R+L+   GL A ++   +      +I P    +G Y+      +  
Sbjct: 183 VQGQSSGQPFAVSCRWLINAGGLFAQQLAHSIDCYPAALIPPLHYCQGRYF--SYSGSSP 240

Query: 236 VNHLIYPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTP 295
             HL+YP+P+P+   LGVH T  + G +  GP              DV  +D        
Sbjct: 241 FRHLVYPMPEPNAVGLGVHATLDLGGQLRFGP--------------DVRYTDSIDYQVDA 286

Query: 296 GILKVLAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKL 355
           G  +  A++                    +Q+Y P      L P  AGVRA+ +S  G  
Sbjct: 287 GSGESFARS--------------------IQRYWPECRAERLQPGYAGVRAK-LSGPGAA 325

Query: 356 IDDFLFVNTA-----RSVNVCNAPSPAATSAIPI 384
             DF+    A       V++    SP  T+++ +
Sbjct: 326 AADFMIQGPAIHGLQGVVSLFGIESPGLTASLAL 359


Lambda     K      H
   0.321    0.137    0.409 

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: 394
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 416
Length of database: 370
Length adjustment: 31
Effective length of query: 385
Effective length of database: 339
Effective search space:   130515
Effective search space used:   130515
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 24 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