GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Herbaspirillum seropedicae SmR1

Align ATPase (characterized, see rationale)
to candidate HSERO_RS05835 HSERO_RS05835 arginine ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__HerbieS:HSERO_RS05835
          Length = 242

 Score =  256 bits (653), Expect = 4e-73
 Identities = 134/241 (55%), Positives = 171/241 (70%), Gaps = 1/241 (0%)

Query: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80
           MI  + + K +G   + L  VSL+V +GEVV ++GPSGSGKST LR +N LES++RG+I 
Sbjct: 1   MIEVKRISKCFGRH-EVLKDVSLSVAQGEVVCLIGPSGSGKSTVLRCINGLESYERGDIL 59

Query: 81  IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140
           I+G R+  D  DI  +R  VGMVFQ+FNLFPH TVL+N+   P+ V     AQA + A  
Sbjct: 60  IDGQRVDRDGPDIHRLRTRVGMVFQRFNLFPHRTVLENVTEGPIYVNGLARAQARSEAMS 119

Query: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200
           LL++V +A + D YP QLSGGQQQRVAIAR+LAMQP  +LFDEPTSALDPE+V EVL VM
Sbjct: 120 LLDKVGLAARCDAYPAQLSGGQQQRVAIARSLAMQPEAILFDEPTSALDPELVGEVLAVM 179

Query: 201 RDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260
           R LA++GMTM+V THE+GFAREVADRV  +  G IVE     +    PQ  R + FL ++
Sbjct: 180 RTLAADGMTMIVVTHEMGFAREVADRVCFLHSGSIVESGAAAQVLAEPQHARTQDFLRRV 239

Query: 261 L 261
           +
Sbjct: 240 I 240


Lambda     K      H
   0.321    0.134    0.387 

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: 208
Number of extensions: 6
Number of successful extensions: 1
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: 261
Length of database: 242
Length adjustment: 24
Effective length of query: 237
Effective length of database: 218
Effective search space:    51666
Effective search space used:    51666
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 (21.9 bits)
S2: 46 (22.3 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