GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Methylobacterium nodulans ORS 2060

Align Putative amino-acid binding periplasmic protein (characterized, see rationale)
to candidate WP_015933040.1 MNOD_RS31675 transporter substrate-binding domain-containing protein

Query= uniprot:Q92PA9
         (260 letters)



>NCBI__GCF_000022085.1:WP_015933040.1
          Length = 256

 Score =  182 bits (461), Expect = 8e-51
 Identities = 101/255 (39%), Positives = 147/255 (57%), Gaps = 6/255 (2%)

Query: 3   ISRRLAATASAAVFVLMAGVAMAEGEKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALC 62
           +SR L   + AA  V  A +     + V I TEG  PPFN +E DG   GF++D+A+ALC
Sbjct: 5   LSRLLVLVSLAASPVQAAPLP----DPVRIATEGGNPPFNYVE-DGKPAGFEVDLAEALC 59

Query: 63  EEMKAECTFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPK 122
           +     C  V   WDGII  L   ++DAI+AS++IT +R+ ++ F+  YY  P + +  +
Sbjct: 60  KAAGLTCRIVLHQWDGIIRGLEGAEYDAIMASLAITPKRRSRISFSRSYYRIPSSYMARR 119

Query: 123 DSPITEATAAALSGKALGAQGSTTHSNYAEAHMKESEVKLYPTADEYKLDLANGRIDAAI 182
           D        AAL G+A+GA   +    Y EA   E++++ + +  +   DL  GR+D  +
Sbjct: 120 DDQTGPLDPAALKGRAVGAAAHSPQLAYLEARAPEADIRSFDSVKDAGYDLRLGRLDLVL 179

Query: 183 DDVVVLSEWLKTEDG-ACCKLLGTLPIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRA 241
            D   L+E L   DG ACC+L+G +P    + GEG GI +RKGDDALRE  ++AI A+ A
Sbjct: 180 GDKRELTEILALPDGAACCRLVGDVPPGDPLLGEGVGIGLRKGDDALREAFDRAIAAVIA 239

Query: 242 NGKYKQINEKYFPFD 256
           +G Y +I  KY PFD
Sbjct: 240 DGTYDRIRAKYLPFD 254


Lambda     K      H
   0.315    0.132    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: 193
Number of extensions: 9
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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