GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Pseudomonas putida KT2440

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Putida:PP_0411
          Length = 374

 Score =  229 bits (584), Expect = 1e-64
 Identities = 134/301 (44%), Positives = 180/301 (59%), Gaps = 18/301 (5%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           +  R V K+Y  G    +K++ L I  GEFL L+GPSG GK+T +  +AG ET + G I 
Sbjct: 15  VSFRGVQKSYD-GESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQ 73

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           +    I+ + P  RDI MVFQ+YAL+P M+V +N+AF L +R +   +I E V RV  ++
Sbjct: 74  LGGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMV 133

Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           Q++    R PGQLSGGQQQRVA+ RAL   P++ L DEPL  LD +LR  M+ E+K +HQ
Sbjct: 134 QLDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQ 193

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243
           RL  T VYVTHDQ EA+T+ D+VAV   G IQQ   P+ +Y  P N FVA+FIG      
Sbjct: 194 RLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGEN---- 249

Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQ------DAGLEDREVILGIRPEQIILANGE 297
                 R  G LLA  D  + + +LP G +      + G     V L IRPE++ L NG 
Sbjct: 250 -----NRISGTLLA-SDGKRCQVQLPRGERVEALAVNVGQAGEPVTLSIRPERVRL-NGH 302

Query: 298 A 298
           +
Sbjct: 303 S 303


Lambda     K      H
   0.319    0.138    0.393 

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: 366
Number of extensions: 12
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: 386
Length of database: 374
Length adjustment: 30
Effective length of query: 356
Effective length of database: 344
Effective search space:   122464
Effective search space used:   122464
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: 50 (23.9 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