GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Catellicoccus marimammalium M35/04/3

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_009488057.1 C683_RS00230 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_03040
         (254 letters)



>NCBI__GCF_000313915.1:WP_009488057.1
          Length = 255

 Score =  132 bits (332), Expect = 7e-36
 Identities = 82/242 (33%), Positives = 135/242 (55%), Gaps = 22/242 (9%)

Query: 4   LEVQDLHKRYGSH----EVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59
           L VQ+L K YG+     + L+ +      G+ + I+G SGSGKST L CI  LE+P +G 
Sbjct: 6   LRVQNLEKYYGNKSQMTKALENIEFSVEEGEFVGIMGPSGSGKSTLLNCIATLERPTSGT 65

Query: 60  ILLNNEELKLVANKDGALKAADPKQLQRMRSR-LSMVFQHFNLWSHMTAMENIMEAPVHV 118
           + LN E          A+     ++L+++R   L  +FQ +NL S +TA ENI  + + +
Sbjct: 66  VCLNGE----------AIDYRKERKLEKIRKEHLGFIFQEYNLLSTLTAYENIALS-LTI 114

Query: 119 LGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178
              S +  +++  L   ++G+      YP  +SGG+QQRVA ARAL   P+++L DEPT 
Sbjct: 115 QNQSPSTIQKRISLLAQQLGIQEILGKYPAELSGGQQQRVAAARALVKNPDLILADEPTG 174

Query: 179 ALDPELVGDVLKVMQALAQEGR-TMVVVTHEMGFAREVSNQLVFLHKG----VVEESGNP 233
           ALD +    +L+ ++ L QE + T+++VTH+  F    + +++F+  G     +E+  + 
Sbjct: 175 ALDSKSAYQLLEQLEVLQQENQATILMVTHD-AFTASFAQRILFIKDGKIFSEIEKGNDT 233

Query: 234 RE 235
           RE
Sbjct: 234 RE 235


Lambda     K      H
   0.317    0.131    0.364 

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: 147
Number of extensions: 6
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: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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: 47 (22.7 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