GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Herbaspirillum seropedicae SmR1

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS20055 HSERO_RS20055 metal-dependent hydrolase

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__HerbieS:HSERO_RS20055
          Length = 597

 Score =  199 bits (505), Expect = 2e-55
 Identities = 116/260 (44%), Positives = 159/260 (61%), Gaps = 10/260 (3%)

Query: 10  PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69
           PLL V+ +  RFGGLVAVNDVSF    GEI  +IGPNGAGK+T FN +TG    + GR+ 
Sbjct: 344 PLLEVDQINKRFGGLVAVNDVSFKVKAGEIVGLIGPNGAGKSTTFNLVTGLLHASGGRVG 403

Query: 70  LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSI 129
               D     +  +P   I+ +  +ARTFQ++RL  GM+VLEN+ +  H +     GF  
Sbjct: 404 FNGRD-----IAGLPARAIA-RLGIARTFQHVRLLPGMTVLENVALGAHMR--SQQGFLK 455

Query: 130 AGLLGLPSYTRTEREA-VDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPV 188
             +  +    R E +A +D A   L RV L      +AGNL  G QR LEIARA+C +P+
Sbjct: 456 NTVNAMLHLERAEEQALLDEAARALHRVGLQHLMHEQAGNLALGQQRILEIARALCCDPL 515

Query: 189 MLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKI 248
           +L LDEPAAGL   E   L+ +L  +R +  + +LL+EHDM  VM ++DH+VV+++G KI
Sbjct: 516 LLLLDEPAAGLRHLEKQALSKVLQELRAD-GMSILLVEHDMEFVMELTDHIVVMEFGAKI 574

Query: 249 SDGDPAFVKNDPAVIRAYLG 268
           ++G P  +   PAVI AYLG
Sbjct: 575 AEGTPQEIARHPAVIEAYLG 594


Lambda     K      H
   0.319    0.137    0.397 

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: 424
Number of extensions: 27
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: 294
Length of database: 597
Length adjustment: 31
Effective length of query: 263
Effective length of database: 566
Effective search space:   148858
Effective search space used:   148858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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