GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Oscillibacter ruminantium GH1

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_040662046.1 ON16_RS10305 NADP-specific glutamate dehydrogenase

Query= BRENDA::P24295
         (450 letters)



>NCBI__GCF_000307265.1:WP_040662046.1
          Length = 450

 Score =  617 bits (1592), Expect = 0.0
 Identities = 300/449 (66%), Positives = 361/449 (80%), Gaps = 1/449 (0%)

Query: 1   MSKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIE 60
           M+ Y+ RV+   + K ++EPEF+QTVEEVLSSL PV+DAHPEYE+ ALLER+V PER IE
Sbjct: 1   MNAYLARVLEATKAKNSNEPEFLQTVEEVLSSLEPVIDAHPEYEKAALLERIVEPERTIE 60

Query: 61  FRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTL 120
           FRV WEDDN    VN GYRVQ+NGA+GPYKGG+RF PSVNLSI+KFLGFEQ FKD++T L
Sbjct: 61  FRVTWEDDNHNWQVNRGYRVQYNGALGPYKGGIRFDPSVNLSIIKFLGFEQVFKDAMTGL 120

Query: 121 PMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQ 180
           P+GGAKGGSDFDP GKSD EVMRFCQAF++ELYRHIG DID PAGDLG G REIGYMYGQ
Sbjct: 121 PIGGAKGGSDFDPRGKSDAEVMRFCQAFISELYRHIGQDIDCPAGDLGCGGREIGYMYGQ 180

Query: 181 YRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFG 240
           YR++VG    G L+GKA   GGS++RPEATGYG+VYY+   + H+  ++ GK +A++G+G
Sbjct: 181 YRRLVGASEFGALSGKAVCTGGSILRPEATGYGAVYYLVEALAHDGQSIEGKRIAMSGYG 240

Query: 241 NVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKF 300
           NV WG  KK  ELGAK    +GPDGYI+DP+G++T+EK+N++LEMRA      + YA+KF
Sbjct: 241 NVGWGIMKKAKELGAKVTYFAGPDGYIHDPDGVSTDEKLNFILEMRAKDPMHCKPYAEKF 300

Query: 301 GVQFFPGEKPWGQK-VDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFL 359
           G +F  G+K WG K VDI MP ATQNDV ++ AK I  + VKYYIEVANMPTTN+AL FL
Sbjct: 301 GCEFVEGKKCWGVKDVDIYMPAATQNDVKMDSAKLIAESGVKYYIEVANMPTTNDALEFL 360

Query: 360 MQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAE 419
            +Q +MVVAPSKAVNAGGV VS  EM+QN+ERL WTAEEVD KL  +M +I+  S   +E
Sbjct: 361 KEQKHMVVAPSKAVNAGGVSVSELEMAQNAERLYWTAEEVDEKLKGIMKNIYHSSVEVSE 420

Query: 420 RYGLGYNLVAGANIVGFQKIADAMMAQGI 448
           RYGLGY+LVAGANIVGFQK+ADAMMAQGI
Sbjct: 421 RYGLGYDLVAGANIVGFQKVADAMMAQGI 449


Lambda     K      H
   0.317    0.136    0.399 

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: 728
Number of extensions: 33
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 (21.6 bits)
S2: 51 (24.3 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