GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas fluorescens FW300-N1B4

Align ATPase (characterized, see rationale)
to candidate Pf1N1B4_4804 ABC-type polar amino acid transport system protein, ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4804
          Length = 254

 Score =  244 bits (624), Expect = 1e-69
 Identities = 125/251 (49%), Positives = 177/251 (70%), Gaps = 11/251 (4%)

Query: 20  TMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEI 79
           +++ A  + K+Y + F AL  +++ V++GEV+ ++GPSGSGKST LR +N LE   +G +
Sbjct: 3   SIVKAVSLNKYY-DHFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGL 61

Query: 80  WIEGHRLSH----------DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRW 129
           W++G  + +          +   IA  R   GMVFQ+FNLFPH+TVLQN++  P QV + 
Sbjct: 62  WVDGELVGYRIVGNKLHELNESQIARQRLATGMVFQRFNLFPHMTVLQNIIEGPCQVLKR 121

Query: 130 PVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALD 189
              +A   A +LL RV +A++ + YP +LSGGQQQRVAIARALAM+P+++LFDEPTSALD
Sbjct: 122 SPKEAHEEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALD 181

Query: 190 PEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQ 249
           PE+V EVL VMRDLA  GMTM+V THE+GFAREV++R+V M +GQIVE   P+    +PQ
Sbjct: 182 PELVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDEGQIVEAGSPEEILISPQ 241

Query: 250 SDRAKQFLAQI 260
           + R + F++ +
Sbjct: 242 NPRTQSFISAV 252


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: 216
Number of extensions: 5
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: 261
Length of database: 254
Length adjustment: 24
Effective length of query: 237
Effective length of database: 230
Effective search space:    54510
Effective search space used:    54510
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: 47 (22.7 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