GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Shewanella loihica PV-4

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 5210878 Shew_3304 ABC transporter-related protein (RefSeq)

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__PV4:5210878
          Length = 292

 Score =  103 bits (257), Expect = 5e-27
 Identities = 84/270 (31%), Positives = 130/270 (48%), Gaps = 26/270 (9%)

Query: 10  PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69
           PL+ + HL    G  V  +DVS +   G++TAI+GP+G GKTTL   I G   P  G + 
Sbjct: 29  PLVEISHLGFSRGTHVIYDDVSLTIPRGKVTAIMGPSGIGKTTLLKLIGGQLRPDSGVIK 88

Query: 70  LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVA--QHNKLIRASGF 127
           +   D  +    R   + + ++ S+   FQ+  LF  M+V +N+  A  +H+ L  A   
Sbjct: 89  VDGVDVHK--CNRSELFALRKRMSML--FQSGALFTDMNVFDNVAFALREHSDLPEAIIR 144

Query: 128 SIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187
            I                  L K  L+ V L   A      L  G QRR  +ARA+  EP
Sbjct: 145 RIV-----------------LMK--LEAVGLRGAAQMMPSELSGGMQRRAALARAIALEP 185

Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247
            ++  DEP AG +P   G L  L+  + D   +  +++ HD+  V+ I+D+V VL   + 
Sbjct: 186 ELVLYDEPFAGQDPISMGVLVKLIRELSDALSLTSVVVSHDVQEVLGIADYVYVLADKKV 245

Query: 248 ISDGDPAFVK-NDPAVIRAYLGEEEDEELP 276
           I+ G PA +K  D   ++ ++G E D  +P
Sbjct: 246 IAHGTPAELKAADNPKLKQFIGGEPDGPVP 275


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: 178
Number of extensions: 12
Number of successful extensions: 2
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: 292
Length adjustment: 26
Effective length of query: 268
Effective length of database: 266
Effective search space:    71288
Effective search space used:    71288
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: 48 (23.1 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