GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Pseudomonas simiae WCS417

Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate GFF5097 PS417_26115 glutamine ABC transporter ATP-binding protein

Query= uniprot:Q88GX0
         (260 letters)



>FitnessBrowser__WCS417:GFF5097
          Length = 241

 Score =  341 bits (875), Expect = 7e-99
 Identities = 173/241 (71%), Positives = 198/241 (82%)

Query: 20  LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79
           +++I GLNK YG F VL  IDL V +GERIVLCGPSGSGKSTLIRCI+RLEVA  G I+ 
Sbjct: 1   MVQISGLNKWYGNFQVLHAIDLTVSQGERIVLCGPSGSGKSTLIRCISRLEVADSGVIRA 60

Query: 80  DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139
              DL   +    +   +IGMVFQ+FNLFPHM+VL NC LAP SVRG SRK AE  AR +
Sbjct: 61  LDADLGKPSPARHKALREIGMVFQNFNLFPHMTVLQNCTLAPMSVRGFSRKRAEAHARHF 120

Query: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199
           L KVGIE+QA+KYPSQLSGGQQQRVAIARALCM+P+IMLFDEPTSALDPEMV EVLDV+V
Sbjct: 121 LDKVGIENQANKYPSQLSGGQQQRVAIARALCMEPKIMLFDEPTSALDPEMVKEVLDVIV 180

Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQIL 259
            LA TGMTMLCVTHEMGFARQVAERVLFL+ G+I+ED PP+ FF  P+++RA+AFLAQI 
Sbjct: 181 TLADTGMTMLCVTHEMGFARQVAERVLFLDAGRIVEDLPPEQFFTAPKSDRAQAFLAQIH 240

Query: 260 H 260
           H
Sbjct: 241 H 241


Lambda     K      H
   0.322    0.137    0.395 

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: 249
Number of extensions: 7
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: 260
Length of database: 241
Length adjustment: 24
Effective length of query: 236
Effective length of database: 217
Effective search space:    51212
Effective search space used:    51212
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