GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adiA in Haloterrigena daqingensis JX313

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_076579764.1 BB347_RS16365 pyruvoyl-dependent arginine decarboxylase

Query= BRENDA::D4GTI7
         (157 letters)



>NCBI__GCF_001971705.1:WP_076579764.1
          Length = 159

 Score =  164 bits (414), Expect = 8e-46
 Identities = 87/160 (54%), Positives = 111/160 (69%), Gaps = 4/160 (2%)

Query: 1   MNTIRVVRGVGTAPTEMASYDAALAAANIHNYNLVAVSSVVPADATVEAVDVAPDLGPAG 60
           M+TIR+V G  +APT M+SYDAALA A + NYNLV+VSSV+PAD  VEAV  APDLGPAG
Sbjct: 1   MSTIRIVWGAASAPTAMSSYDAALADAGVENYNLVSVSSVIPADTHVEAVGTAPDLGPAG 60

Query: 61  NRLTVVQARETTATPGETVVAGLGWATG--SGPGLFYEASG-TDEDSVRAAVIDGLEAGR 117
            RLTVV+AR T   PG    A L W+    +GPGLFYE SG TD + V   V++GL AG+
Sbjct: 61  ERLTVVEARATVTGPGR-ASAALAWSQSVENGPGLFYETSGETDSEDVERRVLEGLAAGQ 119

Query: 118 NLREWSFDDEEVALTTGTHEGEGYTTAVTVAAYGQSESVF 157
            LR+W F D +VA  +   +   +TTA+ +A YG+SE ++
Sbjct: 120 ELRDWEFADAQVATESIQAKSGEHTTALVLAVYGESEPIW 159


Lambda     K      H
   0.311    0.127    0.360 

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: 108
Number of extensions: 7
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: 157
Length of database: 159
Length adjustment: 17
Effective length of query: 140
Effective length of database: 142
Effective search space:    19880
Effective search space used:    19880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 43 (21.2 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