GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Bacteroides clarus YIT 12056

Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate WP_009123266.1 BUB52_RS02110 NADP-specific glutamate dehydrogenase

Query= curated2:B2RKJ1
         (445 letters)



>NCBI__GCF_900129655.1:WP_009123266.1
          Length = 445

 Score =  557 bits (1435), Expect = e-163
 Identities = 270/445 (60%), Positives = 343/445 (77%), Gaps = 2/445 (0%)

Query: 1   MKTQEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFR 60
           M   +++  L+ + P E E+ QAV+EVL ++EE YN+HPEF+K  +IER+  PDRV+ FR
Sbjct: 1   MNAAKVLEDLKRRFPNEPEYHQAVEEVLSTIEEEYNKHPEFDKANLIERLCIPDRVYQFR 60

Query: 61  VPWVDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPM 120
           V WVDD+G VQ N+GYRVQ NNAIGPYKGGIRFH SVNLSILKFL FEQ FKN+LTTLPM
Sbjct: 61  VTWVDDKGNVQTNMGYRVQHNNAIGPYKGGIRFHASVNLSILKFLAFEQTFKNSLTTLPM 120

Query: 121 GGGKGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYK 180
           GGGKGG+DFSP+GKS AE+MRF Q+FM ELWR+IGP+TD+PAGDIGVGGREVG+MFGMYK
Sbjct: 121 GGGKGGSDFSPRGKSNAEVMRFVQAFMLELWRHIGPETDVPAGDIGVGGREVGFMFGMYK 180

Query: 181 KLAREHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVA 240
           KL  E TGT TGKG EFGGS +RPE+TG+G +YF+  M K  G D KGKT  ISG GNVA
Sbjct: 181 KLTHEFTGTFTGKGREFGGSLIRPEATGYGNIYFLLEMLKTKGTDLKGKTCLISGSGNVA 240

Query: 241 WGVAQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNA 300
              A+K  E+G KV+T+S  DGY+YDP GI+  EK   +++L++     + +Y +++P  
Sbjct: 241 QYTAEKVLEMGGKVLTMSDSDGYIYDPAGIDR-EKLDYIMELKNLYRGRIREYAEQYPGV 299

Query: 301 QFFPGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVAN 360
           ++  G +PW +K D A+P ATQNE+N +DA+ L  NGV  V+E +NM  T EA + +   
Sbjct: 300 KYVEGARPWSEKADIALPSATQNEINGDDARKLIANGVMAVSEGANMPSTPEAIKVFQEA 359

Query: 361 KMLFAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGN- 419
           K+L+APGKA NAGGVS SGLEMTQN++ L W++EEVD+ L  IM++IH  CV YG + N 
Sbjct: 360 KILYAPGKAANAGGVSVSGLEMTQNSIKLGWSSEEVDEKLKSIMKNIHAACVQYGTEENG 419

Query: 420 YIDYVKGANIAGFMKVAKAMVAQGV 444
           Y++YVKGAN+AGFMKVAKAM+AQG+
Sbjct: 420 YVNYVKGANVAGFMKVAKAMMAQGI 444


Lambda     K      H
   0.319    0.137    0.417 

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: 724
Number of extensions: 40
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: 445
Length of database: 445
Length adjustment: 32
Effective length of query: 413
Effective length of database: 413
Effective search space:   170569
Effective search space used:   170569
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 (21.7 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