GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Paraburkholderia bryophila 376MFSha3.1

Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate H281DRAFT_04050 H281DRAFT_04050 beta-aspartyl-peptidase (threonine type)

Query= BRENDA::P37595
         (321 letters)



>FitnessBrowser__Burk376:H281DRAFT_04050
          Length = 331

 Score =  360 bits (925), Expect = e-104
 Identities = 189/327 (57%), Positives = 232/327 (70%), Gaps = 18/327 (5%)

Query: 4   AVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEEC 63
           AVIAIHGGAG I RA +S   E  Y  AL A++  GQ++L  G SALD V+EAVRLLE+C
Sbjct: 5   AVIAIHGGAGTILRASLSASAEAEYHAALHAVLAAGQRVLADGGSALDAVSEAVRLLEDC 64

Query: 64  PLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMI 123
           PLFNAG GAV+T   THELDA +MDG+TL+AGA+  V  +RNPVLAAR V+E S HV+  
Sbjct: 65  PLFNAGRGAVYTAAGTHELDAAIMDGSTLEAGAICCVKRVRNPVLAARRVLECSEHVLFA 124

Query: 124 GEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGA-------------- 169
           GEGAE+FA A+G+E V P+ F T  R  Q L AR +   +LDH GA              
Sbjct: 125 GEGAESFAAAQGLEFVEPQYFDTEARLRQWLLARDQQRAMLDHDGASLAASPSATDNSDP 184

Query: 170 ----PLDEKQKMGTVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASV 225
               P+D  +K GTVGAVALD  G++AAATSTGG+TNK  GRVGD+PL+GAGCYA++A+ 
Sbjct: 185 VPHEPIDPNRKFGTVGAVALDRHGHVAAATSTGGVTNKQVGRVGDTPLIGAGCYADDATC 244

Query: 226 AVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGN 285
           AVS TG+GE+F+R +AAYD+AA M Y  +SL EA   VVM +LP + G GGLIA+D  GN
Sbjct: 245 AVSTTGSGEMFMRMVAAYDVAAQMAYRNVSLQEAAHDVVMNRLPKIDGRGGLIAVDALGN 304

Query: 286 VALPFNTEGMYRAWGYAGDTPTTGIYR 312
           +ALPFNTEGMYR +   G+ PTT IYR
Sbjct: 305 IALPFNTEGMYRGFARIGEAPTTAIYR 331


Lambda     K      H
   0.316    0.133    0.377 

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: 376
Number of extensions: 14
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: 321
Length of database: 331
Length adjustment: 28
Effective length of query: 293
Effective length of database: 303
Effective search space:    88779
Effective search space used:    88779
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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