GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Kocuria turfanensis HO-9042

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_062735050.1 AYX06_RS06345 NADP-specific glutamate dehydrogenase

Query= BRENDA::P24295
         (450 letters)



>NCBI__GCF_001580365.1:WP_062735050.1
          Length = 446

 Score =  454 bits (1167), Expect = e-132
 Identities = 229/432 (53%), Positives = 298/432 (68%), Gaps = 7/432 (1%)

Query: 19  EPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGY 78
           E EF Q V+EV  SLGPVV  HPE+ + A+LER+  PER I FRVPW DD G+VH+N G+
Sbjct: 19  EVEFHQAVDEVFDSLGPVVARHPEFLDAAVLERICEPERQIIFRVPWTDDEGRVHINRGF 78

Query: 79  RVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSD 138
           RV+FN A+GPYKGGLRF PSV L I+KFLGFEQ FK++LT +P+GG KGGSDFDP+G+SD
Sbjct: 79  RVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNALTGMPIGGGKGGSDFDPSGRSD 138

Query: 139 REVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKAR 198
            E+MRFCQ+FMTELYRHIG   DVPAGD+GVG REIGY++GQY++I   + +GVLTGK  
Sbjct: 139 AEIMRFCQSFMTELYRHIGEYTDVPAGDIGVGGREIGYLFGQYKRITNRYESGVLTGKGL 198

Query: 199 SFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAV 258
           S+GGSLVR EATGYG+V + E +++    +  G+TV ++G GNVA  A  +   LGA  +
Sbjct: 199 SWGGSLVRTEATGYGTVMFAEEMLRTRGQSFDGQTVLVSGSGNVATFAIARAQHLGATVI 258

Query: 259 TLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFG--VQFFPGEKPWGQKVD 316
           T S   G + DP+GI  E     + +++   R ++ +YA++ G   +F      W     
Sbjct: 259 TASDSGGCVVDPDGIDLE----LLRQIKEVERGRISEYAERRGGRARFIAKGSVWDVPGT 314

Query: 317 IIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAG 376
           + +PCATQN++D   AKK++A+ V    E ANMP+T EA R + Q+  ++  P KA NAG
Sbjct: 315 VALPCATQNELDGSHAKKLLAHGVVAVAEGANMPSTGEATR-MFQEAGVLFGPGKAANAG 373

Query: 377 GVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGF 436
           GV  S  EM QN+ R SWT    + +L Q+MT IHD  A  AE YG+  N VAGANI GF
Sbjct: 374 GVATSALEMQQNASRDSWTFGYTEERLGQIMTSIHDRCAETAEDYGMPGNYVAGANIAGF 433

Query: 437 QKIADAMMAQGI 448
            K+A AMMAQG+
Sbjct: 434 VKVAGAMMAQGL 445


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: 616
Number of extensions: 22
Number of successful extensions: 3
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: 446
Length adjustment: 33
Effective length of query: 417
Effective length of database: 413
Effective search space:   172221
Effective search space used:   172221
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