GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Methylobacterium nodulans ORS 2060

Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_015933040.1 MNOD_RS31675 transporter substrate-binding domain-containing protein

Query= TCDB::O50181
         (259 letters)



>NCBI__GCF_000022085.1:WP_015933040.1
          Length = 256

 Score =  134 bits (338), Expect = 1e-36
 Identities = 91/258 (35%), Positives = 133/258 (51%), Gaps = 12/258 (4%)

Query: 1   MKKLALLGALALSVLSLPTFAAD--KPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALC 58
           + +L +L +LA S    P  AA    PVRI  E   PPF+    DG+ AGF+VD+  ALC
Sbjct: 5   LSRLLVLVSLAAS----PVQAAPLPDPVRIATEGGNPPFNY-VEDGKPAGFEVDLAEALC 59

Query: 59  EEMKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKE 118
           +   + C+ V  ++DG+I  L+  + DAI++S+ IT +R+  + F+  YY  P+ ++ + 
Sbjct: 60  KAAGLTCRIVLHQWDGIIRGLEGAEYDAIMASLAITPKRRSRISFSRSYYRIPSSYMARR 119

Query: 119 GASLN--DPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLD 176
                  DP A LKG+  G    S    Y  A    A  ++  ++S ++A  DL  GRLD
Sbjct: 120 DDQTGPLDPAA-LKGRAVGAAAHSPQLAYLEARAPEA--DIRSFDSVKDAGYDLRLGRLD 176

Query: 177 AVVADSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDA 236
            V+ D   L +     D       VG         GEGVGI +RKGD  L   F+ AI A
Sbjct: 177 LVLGDKRELTEILALPDGAACCRLVGDVPPGDPLLGEGVGIGLRKGDDALREAFDRAIAA 236

Query: 237 LRANGKYKQIQDKYFSFD 254
           + A+G Y +I+ KY  FD
Sbjct: 237 VIADGTYDRIRAKYLPFD 254


Lambda     K      H
   0.316    0.135    0.381 

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: 184
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: 259
Length of database: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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