GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Pseudomonas simiae WCS417

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF4516 PS417_23115 carbon-nitrogen hydrolase

Query= reanno::pseudo1_N1B4:Pf1N1B4_2504
         (264 letters)



>FitnessBrowser__WCS417:GFF4516
          Length = 263

 Score = 89.4 bits (220), Expect = 7e-23
 Identities = 78/244 (31%), Positives = 115/244 (47%), Gaps = 21/244 (8%)

Query: 1   MRVALYQCPPLPLDVAGNLQRLHQLALEAKGADLLVLPEMFLTGYNIGIDAVS--VLAEV 58
           + +AL Q      D   NL+    L  +A+GADL+VLPEMF TG+++    ++       
Sbjct: 10  LNIALVQTNLAWHDRQANLEHFELLLEQAQGADLIVLPEMFTTGFSMESQTLAEPEYGPA 69

Query: 59  HNGESAQQIARIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLFGDL- 117
           H+   AQ     A  TG  I+     +  DG   N +     +GE L +Y K HLF    
Sbjct: 70  HHWLQAQAAKYNAVITGSVII-----QAADGSHRNRLLWARPDGEVL-HYDKRHLFRMAG 123

Query: 118 DHSMFSPGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILV----PTANMIP 173
           +H+ ++PG  +    EL GW++  LICYDL FP  +R       +L+L     P A    
Sbjct: 124 EHNHYTPGERQVQF-ELKGWRIRPLICYDLRFPVWSR--DAQDTDLLLYTANWPGARRSH 180

Query: 174 YDFIADVTVRARAFENQCYVAYANYCGHEGE-IQYCGQSSIAAPDGSRIAQAGLDEALIV 232
           ++ +    + ARA EN CYVA  N  G +G+   Y G S +    G  +  AG  + +  
Sbjct: 181 WNRL----LPARAIENLCYVAAVNRVGTDGKGFAYTGDSQVLDFQGETLLSAGEADGVFQ 236

Query: 233 GELD 236
             LD
Sbjct: 237 VNLD 240


Lambda     K      H
   0.322    0.140    0.420 

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: 189
Number of extensions: 14
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: 264
Length of database: 263
Length adjustment: 25
Effective length of query: 239
Effective length of database: 238
Effective search space:    56882
Effective search space used:    56882
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