GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas litoralis 2SM5

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_900105005.1:WP_090273343.1
          Length = 404

 Score =  221 bits (563), Expect = 3e-62
 Identities = 143/399 (35%), Positives = 219/399 (54%), Gaps = 40/399 (10%)

Query: 26  VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85
           ++  R + S +WD +GREYID AGGIAV + GH HP+++ A+ EQ  KL H    ++  E
Sbjct: 25  MIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVS-NIMTNE 83

Query: 86  PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-ATGRAG-----VIAFTGAY 139
           P + LA+++   V   F  K L V SG+EA E A K+AR  A  ++G     +IA + ++
Sbjct: 84  PALRLADKL---VAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKHEIIACSNSF 140

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199
           HGRT+ T+ + G+   YS G G    GI               + IA++E         +
Sbjct: 141 HGRTLFTVSVGGQP-KYSQGFGPAISGISHV----------PYNDIAALEAQIS-----E 184

Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259
              A+++EPVQGEGG    S  +++ +RALCD++  LLI DEVQ+G GRTG  +A    G
Sbjct: 185 RTCAVVVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSG 244

Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319
           + PD+ T AK +GGGFPI+ +     +  A++ G  G TY G+P+ CA A  VL +    
Sbjct: 245 VAPDILTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTP 304

Query: 320 KLLERSQAVGER---LKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSK 376
           ++L+    VGER   L AGLR +  +  V  ++RG G ++   L E             +
Sbjct: 305 QVLD---GVGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQ------AGQ 355

Query: 377 IVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415
           ++  A+E+GL++L  G   +V+R    + IP+A + + L
Sbjct: 356 VMRLAQEEGLLVLQAGA--DVVRLAPSLIIPEADIREAL 392


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: 423
Number of extensions: 20
Number of successful extensions: 4
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: 404
Length adjustment: 31
Effective length of query: 395
Effective length of database: 373
Effective search space:   147335
Effective search space used:   147335
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 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