GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate AO356_28625 AO356_28625 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28625
          Length = 259

 Score =  248 bits (632), Expect = 1e-70
 Identities = 136/255 (53%), Positives = 174/255 (68%), Gaps = 11/255 (4%)

Query: 10  SPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69
           S E II+   V+K +G+  +LK I+L V++GE +VL G SGSGK+T IRC+N LE+ Q G
Sbjct: 5   SEELIIEALDVHKSFGELQILKGISLQVRRGEVVVLIGASGSGKTTFIRCINLLEDIQGG 64

Query: 70  RIVV-----------DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWV 118
           RI V           DG  +    + I   RR++GMVFQ FNLFPH+T L+N   AP+ V
Sbjct: 65  RIRVNGRAMGYRERADGSLVRESERNIARQRRDIGMVFQRFNLFPHMTALENIIEAPIQV 124

Query: 119 RKMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTS 178
             + +  A E A   LERV + ++A  YP  LSGGQQQRVAIARAL MKP+ MLFDEPTS
Sbjct: 125 LGVSRVAALEQARGLLERVGLADKADHYPSMLSGGQQQRVAIARALAMKPQAMLFDEPTS 184

Query: 179 ALDPEMVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFD 238
           ALDPE V EVL  M  LAE+GMTM+ VTHEMGFAR VA+RV+ +D+GE++EQ  P   F 
Sbjct: 185 ALDPETVGEVLQVMKELAEEGMTMVVVTHEMGFAREVADRVVVLDQGELIEQGPPEQIFC 244

Query: 239 NPQNDRTKLFLSQIL 253
           +P + RT+ FLS++L
Sbjct: 245 HPIHPRTRAFLSRVL 259


Lambda     K      H
   0.322    0.137    0.407 

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: 209
Number of extensions: 7
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: 254
Length of database: 259
Length adjustment: 24
Effective length of query: 230
Effective length of database: 235
Effective search space:    54050
Effective search space used:    54050
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