GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Herbaspirillum seropedicae SmR1

Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease

Query= uniprot:A0KWY7
         (320 letters)



>FitnessBrowser__HerbieS:HSERO_RS03645
          Length = 339

 Score =  150 bits (380), Expect = 3e-41
 Identities = 106/312 (33%), Positives = 167/312 (53%), Gaps = 20/312 (6%)

Query: 7   IPLWITASLL---LTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63
           +P+ +   LL   LT++L G      FAS     N+LR  A  L+ A GMT VI++ GID
Sbjct: 30  LPVLVVLYLLFYGLTLYLSGDGT-SNFASAENTMNILRQVAINLVLAAGMTFVILTAGID 88

Query: 64  LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123
           LSVG+V+A+S V+   +       P  A  + +  G + G + G ++ +  +  F+VTL 
Sbjct: 89  LSVGSVLAVSAVLG--MQVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLG 146

Query: 124 GMFLARGLATTLSEESIAI--DHPFYDAVAEMSIALPGNGA-LDLSSLIFILFFVIIA-- 178
            M   RG A  L++ +  +  D P ++ +        GNG  L +  LI++   V++   
Sbjct: 147 TMTAFRGAAYLLADGTTVLNNDIPSFEWI--------GNGDFLHVPWLIWVAVAVVLLSW 198

Query: 179 VVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYA 238
           V++  T  G ++YAIGGN  +A L GI +    + +Y+IS   + LAG +     +    
Sbjct: 199 VILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANG 258

Query: 239 LGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVI 298
               G ELDAIAAVV+GGT L GG G + GTV+G +++GV+   +T  G LSS+W  +  
Sbjct: 259 NWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILG-LSSFWQYVAK 317

Query: 299 GLLLFFFILLQK 310
           G ++   ++L K
Sbjct: 318 GAVIVLAVILDK 329


Lambda     K      H
   0.330    0.145    0.424 

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: 357
Number of extensions: 19
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: 320
Length of database: 339
Length adjustment: 28
Effective length of query: 292
Effective length of database: 311
Effective search space:    90812
Effective search space used:    90812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 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