GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Sulfurivirga caldicuralii DSM 17737

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

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



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  123 bits (308), Expect = 4e-33
 Identities = 87/230 (37%), Positives = 125/230 (54%), Gaps = 18/230 (7%)

Query: 4   LEVQDLHKRY----GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59
           LE ++L K Y        VLKGVSL     + ++I+GSSGSGKST L  +  L++P  G+
Sbjct: 6   LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65

Query: 60  ILLNNEELKLVANKDGALKAADPKQLQRMRSR-LSMVFQHFNLWSHMTAMENIMEAPVHV 118
           +LL  +    +                R+R+R +  V+Q  +L   +TA EN+M  P+ +
Sbjct: 66  VLLLGQPFSKLGEAARG----------RLRNRHMGFVYQFHHLLPELTAEENVM-MPLLI 114

Query: 119 LGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178
              S+A AR+KA   L  VG+S R    P  +SGGE+QRVA+ARAL  EP+ +L DEPT 
Sbjct: 115 RRESEATARDKALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTG 174

Query: 179 ALDPELVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVV 227
            LD      VL +M  L Q  G  ++VVTH++  A  +   L  L  G++
Sbjct: 175 NLDSRSAEQVLSLMDDLNQRFGTALLVVTHDVNIAARMDRTLT-LRDGMI 223


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: 145
Number of extensions: 12
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: 227
Length adjustment: 23
Effective length of query: 231
Effective length of database: 204
Effective search space:    47124
Effective search space used:    47124
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 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