GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Haloterrigena daqingensis JX313

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_076582365.1 BB347_RS07365 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_001971705.1:WP_076582365.1
          Length = 439

 Score =  246 bits (629), Expect = 8e-70
 Identities = 147/410 (35%), Positives = 220/410 (53%), Gaps = 16/410 (3%)

Query: 26  VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85
           V  +RA   T+ D +G EY+D   GI+V N GH +  V+ A ++QL +  H C  V    
Sbjct: 29  VPIKRASGETLEDFDGNEYLDAFSGISVTNVGHNNEAVVEAAKDQLDEFVHGCSYVHPNA 88

Query: 86  PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMM 145
           P  ELAE +A   PGD  K +    SG+EAVE A+K+AR  TG   V+A    +HGRT+ 
Sbjct: 89  PVGELAERLASETPGDLTK-SFFCNSGTEAVEGAIKLARKYTGSTEVLALEMGFHGRTLG 147

Query: 146 TLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIAS------IERIFKNDAQPQ 199
           +L LTG    Y  GM      +     P      S +    +      +ER+        
Sbjct: 148 SLALTGNKA-YKNGMAPTINDVSHVEPPYGYRCPSCEGETCTAACAENVERVIGTHTA-D 205

Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259
           D+AAI++EPV GEGG  V  + +++R++ +  +H  LLIADEVQTG GRTG  +A +   
Sbjct: 206 DLAAIVVEPVMGEGGIIVPPEGWLERVQEIAHEHDALLIADEVQTGYGRTGELWAVDHFD 265

Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319
           +VPD+ T AK +  G P+     + EI DA   G    T+ G+P+ACAAALA L+   ++
Sbjct: 266 VVPDIITQAKGIANGLPLGAFTAREEIADAFESGDHLSTFGGNPVACAAALATLEEL-QD 324

Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFE------GGDTHKPAAEL 373
            +++ ++  G  L+  L  ++++  V+GD RGLG M  +E+ +       G    P A+L
Sbjct: 325 GIIDNAREQGAWLEDELAALESEFDVVGDTRGLGLMYGLEIVDPSTDGPRGVAPAPDAKL 384

Query: 374 VSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFD 423
              +    RE+G+++   G Y NVIR   P+TI  +QLE+ +A L    +
Sbjct: 385 AKSVAADLREEGIVIGVGGYYSNVIRLQPPLTIDRSQLERIVAALRSALE 434


Lambda     K      H
   0.319    0.137    0.393 

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: 466
Number of extensions: 23
Number of successful extensions: 5
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: 426
Length of database: 439
Length adjustment: 32
Effective length of query: 394
Effective length of database: 407
Effective search space:   160358
Effective search space used:   160358
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 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