GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Pseudomonas putida KT2440

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate PP_3846 PP_3846 (R)-stereoselective amidase

Query= BRENDA::B3IVI7
         (264 letters)



>FitnessBrowser__Putida:PP_3846
          Length = 271

 Score =  147 bits (371), Expect = 2e-40
 Identities = 99/257 (38%), Positives = 136/257 (52%), Gaps = 7/257 (2%)

Query: 1   MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEA 60
           M+I L Q + +  D   NL+R   QA         LL+ PE  L G+     Q+  +AE 
Sbjct: 1   MKIELVQLSGRDGDTAYNLERTL-QAIATCAVDTDLLIFPETQLMGF-ASAQQLAEIAEP 58

Query: 61  ADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGELD 120
            +GP+   V        ++ V G  E  D G +YN+  L+   G +LS YRKTHL+   +
Sbjct: 59  VNGPSVQAVQRAVHERNVSAVIGLAEN-DSGTVYNTSLLVTPQGIALS-YRKTHLWPS-E 115

Query: 121 RSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTPYDFTC 180
           R +F  G D +     +G +VG+LICYDIEFPE+AR L   GAELILV   NM PY    
Sbjct: 116 RGLFQQG-DRYVTALWKGIRVGILICYDIEFPESARALGQLGAELILVTNGNMDPYGPVH 174

Query: 181 QVTVRARAQENQCYLVYANYCGAEDE-IEYCGQSSIIGPDGSLLAMAGRDECQLLAELEH 239
           +  + ARAQENQ + V  N  G  DE + + G S+ + P G  L  AGR EC+ + EL+ 
Sbjct: 175 RTAIMARAQENQAFAVMVNRVGDGDEGLVFAGGSAAVDPFGRTLFEAGRAECRQVVELDL 234

Query: 240 ERVVQGRTAFPYLTDLR 256
           + +   R  + YL D R
Sbjct: 235 DLLRTARHEYDYLGDRR 251


Lambda     K      H
   0.322    0.139    0.416 

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: 220
Number of extensions: 11
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: 264
Length of database: 271
Length adjustment: 25
Effective length of query: 239
Effective length of database: 246
Effective search space:    58794
Effective search space used:    58794
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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