GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dadA in Marinobacter adhaerens HP15

Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate GFF2666 HP15_2610 D-amino acid dehydrogenase small subunit

Query= reanno::acidovorax_3H11:Ac3H11_4848
         (445 letters)



>FitnessBrowser__Marino:GFF2666
          Length = 427

 Score =  402 bits (1033), Expect = e-116
 Identities = 202/435 (46%), Positives = 277/435 (63%), Gaps = 20/435 (4%)

Query: 1   MKTIVLGAGIIGISTAWHLLERGHEVIVIDRQPDAALETSFANAAQISVSYCEPWANREA 60
           M  +VLGAG++G +TAW+L ++GH+V V+DRQ  A LETS+AN  QISVS+ EPWAN  A
Sbjct: 11  MHILVLGAGVVGTTTAWYLQKQGHQVTVVDRQNQAGLETSYANGGQISVSHAEPWANPSA 70

Query: 61  PLKALKWMFDKEAPLLFRPQMDWQQWRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALK 120
           PLK +KW+F  +APLLFRP++D  QWRW L FL QC       N++Q+V LG YS + L+
Sbjct: 71  PLKVMKWLFQPDAPLLFRPRLDPAQWRWALSFLGQCTLARAAHNIRQMVNLGTYSCSQLQ 130

Query: 121 DLVGTTGIEYNRLERGIAHFYTDQKSFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFR 180
            L    GIEYN LE+GI HFYT+   FD A     +M+  G  R+++  D  +++EPA +
Sbjct: 131 ALREEAGIEYNHLEKGILHFYTNPAEFDGAMEPTRIMQDLGCDRQIIDADRAVELEPALK 190

Query: 181 AYGDKITGGTYTSTDESGDARVFTQELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVM 240
              ++I G TYTS DESGDAR+FTQ LA+RC   G +F YG ++L   + G  +  +  +
Sbjct: 191 PIRNRIAGATYTSEDESGDARMFTQNLAKRCAEAGVEFRYGTEILSFERAGERVLGIQTL 250

Query: 241 ARQPGGGGKKDFILKADAVVVACGSYSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAPM 300
                  G  +  L+ADA V++ GS+SA L   +G+ L IYP KGYS T P+   E A  
Sbjct: 251 R-----DGHHE-TLRADAYVLSMGSFSAALASQLGIFLNIYPAKGYSITVPVKNEEAAFN 304

Query: 301 VSTIDDGKKIAMSRLGNHLRVAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDT 360
           VS  DD  K+  SRLG+ +RVAGT ELNG+   L+ +    RC  + RR   ++      
Sbjct: 305 VSLTDDEYKLVYSRLGDRMRVAGTAELNGYSRKLNYT----RCRAIVRRTAEVM------ 354

Query: 361 RTPEEG--GDPQYWTGLRPATPTNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAEL 418
             PE G     ++WTGLRPATP+N+P+IG++    L++N GHGTLGWTH  GS  ALA++
Sbjct: 355 --PEAGYWDQAEFWTGLRPATPSNVPYIGKSHFANLYLNTGHGTLGWTHSCGSAAALADI 412

Query: 419 ISGQVPAMNFGFCGM 433
           I G+ P ++F F G+
Sbjct: 413 IDGRKPEVDFTFSGL 427


Lambda     K      H
   0.321    0.137    0.424 

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: 536
Number of extensions: 18
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: 427
Length adjustment: 32
Effective length of query: 413
Effective length of database: 395
Effective search space:   163135
Effective search space used:   163135
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: 51 (24.3 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