GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Algiphilus aromaticivorans DG1253

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_052367418.1 U743_RS01940 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_000733765.1:WP_052367418.1
          Length = 413

 Score =  144 bits (363), Expect = 3e-39
 Identities = 80/230 (34%), Positives = 134/230 (58%), Gaps = 11/230 (4%)

Query: 23  SLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALKAADP 82
           S + A G+V  ++G SGSGKST +R +N L +P +G I LN  ++   + ++        
Sbjct: 48  SFEVAEGEVFVVMGLSGSGKSTLVRMLNRLIEPSSGSIKLNGRDITQASRRE-------- 99

Query: 83  KQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKVGVAHR 142
             ++  R  +SMVFQ F L  H T ++N     ++V GM K E   KA   L+ VG+   
Sbjct: 100 -LIEIRRRSISMVFQSFALMPHQTVLQNAAFG-LNVAGMKKEEREAKAMEALDAVGLKSN 157

Query: 143 KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVL-KVMQALAQEGRT 201
            ++YP  +SGG +QRV +ARALA +PEV+L DE  SALDP +  ++  ++++  +++ RT
Sbjct: 158 ANSYPDELSGGMKQRVGLARALATDPEVLLMDEAFSALDPLIRTEMQDELLRLQSEQART 217

Query: 202 MVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLSG 251
           +V +TH++  A  V +++  +  G + + G P E++  P +E ++ F  G
Sbjct: 218 VVFITHDLDEAMRVGDRIAIMQGGWIVQIGTPEEIVRAPANEYVRSFFRG 267


Lambda     K      H
   0.317    0.131    0.366 

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: 220
Number of extensions: 12
Number of successful extensions: 4
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: 413
Length adjustment: 28
Effective length of query: 226
Effective length of database: 385
Effective search space:    87010
Effective search space used:    87010
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: 48 (23.1 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