GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuD in Lactobacillus silagei IWT126

Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_054654784.1 CES79_RS01835 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein

Query= reanno::Koxy:BWI76_RS10705
         (254 letters)



>NCBI__GCF_002217945.1:WP_054654784.1
          Length = 246

 Score =  107 bits (268), Expect = 2e-28
 Identities = 83/228 (36%), Positives = 112/228 (49%), Gaps = 20/228 (8%)

Query: 32  LNAIVNAGGVPIALPHALAEPELLSALLPKLDGIYLPGSPSNVQPHLYGENGDEPDADPG 91
           + A+V AGGVPI  P    +PE +   L   DG+   G  ++V P  YGE   EP    G
Sbjct: 32  IEAVVKAGGVPIIFPSV--DPEDVGDYLDLFDGVAFLGG-ADVDPTFYGE---EPHEKLG 85

Query: 92  -----RDLLSMALIDAALERRIPIFAICRGLQELVVATGGTLYRRLFEQPEL-LEHREDP 145
                RDL  + L+  A+ +   IF ICRG+Q +    GGT+Y+ L E P++ L+H +  
Sbjct: 86  VTYRKRDLFEIELLKQAVAQGKAIFGICRGMQLINTGLGGTVYQDLSENPDMTLKHNQ-- 143

Query: 146 ELPVEQQYAPSHEVQVQEGGLLSQLIPGCNTFWVNSLHGQGAKTTGPRLRVEARSPDGLA 205
                    PSH V V     L + I G   + VNS H Q  K     L+V AR+ DG+ 
Sbjct: 144 ---AAAGNMPSHHVSVDPTSRLFK-ITGARPY-VNSRHHQAVKQLATSLKVTARADDGVI 198

Query: 206 EAVSVNDHPFALGVQWHPEWNSSEYALSRMLFEGFITACQNYVAEKQR 253
           EA     +   L VQWHPE     +A S+ LF   IT  +  VAE+ R
Sbjct: 199 EAFESTANDQILAVQWHPENMYKHHAESKALFADLITRSRK-VAEQTR 245


Lambda     K      H
   0.318    0.137    0.415 

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: 168
Number of extensions: 11
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: 254
Length of database: 246
Length adjustment: 24
Effective length of query: 230
Effective length of database: 222
Effective search space:    51060
Effective search space used:    51060
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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