GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter related (characterized, see rationale)
to candidate Pf1N1B4_3175 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

Query= uniprot:B2TBJ9
         (263 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3175
          Length = 254

 Score =  300 bits (768), Expect = 2e-86
 Identities = 152/250 (60%), Positives = 197/250 (78%), Gaps = 2/250 (0%)

Query: 9   LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68
           L+++ +HKS+GDH VLKG+SL A  GDVIS++GASGSGKSTFLRC+N LE P+DG++SL 
Sbjct: 4   LTIEGLHKSYGDHQVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSLD 63

Query: 69  GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128
           G+ ++M     G ++ +D  ++ R+R++L MVFQ+FNLWSHMTVLEN+   P RV   S+
Sbjct: 64  GQTIRMIHDRHG-MRVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGCSK 122

Query: 129 AESVEEAEALLAKVGLAEK-RGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDP 187
            E+ + A   L KVGLA +    YPA LSGGQQQRVAIARALAM P+VMLFDEPTSALDP
Sbjct: 123 QEAEDRARRYLDKVGLAARVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDP 182

Query: 188 ELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKS 247
           ELVGEVL+V++ LAEEGRTM++VTHEM FAR VS++V+FLHQG VE +G P++V    KS
Sbjct: 183 ELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEEGAPEDVLGNPKS 242

Query: 248 DRFRQFVSSH 257
           +R +QF+S +
Sbjct: 243 ERLKQFLSGN 252


Lambda     K      H
   0.318    0.133    0.377 

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: 221
Number of extensions: 3
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: 263
Length of database: 254
Length adjustment: 24
Effective length of query: 239
Effective length of database: 230
Effective search space:    54970
Effective search space used:    54970
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 (21.7 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