GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pedobacter sp. GW460-11-11-14-LB5

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__Pedo557:CA265_RS15205
          Length = 378

 Score =  197 bits (500), Expect = 6e-55
 Identities = 124/347 (35%), Positives = 185/347 (53%), Gaps = 36/347 (10%)

Query: 30  RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89
           RA+   ++D + +++ID   GI V N GH HP V+ A+QEQ    + T   ++ Y  Y++
Sbjct: 6   RAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQ----AETYMHLMVYGEYVQ 61

Query: 90  LAE-EIAKRVPGDFPKK---TLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMM 145
             +   AK +    P+    T  + SG+EAVE A+K+A+  TGR G IA   AYHG T  
Sbjct: 62  TPQVNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKGFIACKNAYHGSTQG 121

Query: 146 TLGLTGKVVPYSAGMG-LMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAI 204
              L      YS+G G  +P   F            E +++A +E+I        +IAA+
Sbjct: 122 AESLMESDF-YSSGYGPFLPHVSF-----------IEHNNLADLEKI------TNEIAAV 163

Query: 205 IIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDL 264
            IEP+QGE G  V+  S+MQ LR  C + G LLI DE+Q+G GR+G  FA E   +VPD+
Sbjct: 164 FIEPIQGEAGIRVSDLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDV 223

Query: 265 TTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGG---TYAGSPIACAAALAVLKVFEEEKL 321
              AK +GGG PI       EIM  ++   + G   T+ G P+ CAA LA L+   ++ +
Sbjct: 224 LLLAKGIGGGMPIGAFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHI 283

Query: 322 LERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHK 368
           ++  +  G+  K  L     +H  I ++RG G M+A+E FE  + +K
Sbjct: 284 VDEVEEKGQLFKQLL-----QHPAIKEIRGKGLMLAVE-FENFEINK 324


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: 365
Number of extensions: 12
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: 378
Length adjustment: 31
Effective length of query: 395
Effective length of database: 347
Effective search space:   137065
Effective search space used:   137065
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: 50 (23.9 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