GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Pseudomonas fluorescens FW300-N2E3

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate AO353_03840 AO353_03840 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03840
          Length = 351

 Score =  227 bits (578), Expect = 5e-64
 Identities = 136/334 (40%), Positives = 193/334 (57%), Gaps = 16/334 (4%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           M  +  + + K Y G    +  ++LH+ +G+ V  LGPSGCGK+T+LRMIAGLE +SGG 
Sbjct: 1   MTGLILENVEKRY-GTACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGE 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           +R+    + + PA  RN  MVFQ+ AL+PHM+V +NIA+ L+       +   RV E+  
Sbjct: 60  IRLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELLE 119

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           L+ L+ +++R    +SGGQ+QR AIARAI   P + L DEPLS LDAKLR  ++ +I++L
Sbjct: 120 LIQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQL 179

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGT--- 237
            QRL  TT+ VTHDQ EAMT+AD V+++   R+ Q G+P E+YR+P N F A FIG+   
Sbjct: 180 QQRLNITTIMVTHDQREAMTMADIVVVLGQNRVQQVGTPIEIYRHPANEFVADFIGSGNI 239

Query: 238 -PAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREP 296
            PA     G V    G           AL     S +     VK+ VRP+ ++++  +  
Sbjct: 240 FPATALGDGKVGLPGGD----------ALQVPICSSIVVGEKVKMLVRPEDLQLSHPQAT 289

Query: 297 AASLTCPVSVELVEILGADALLTTRCGDQTLTAL 330
           A +      V  V  +GA    T  C   TLTAL
Sbjct: 290 AGNRLLG-RVTFVRDIGATIETTVECSGVTLTAL 322


Lambda     K      H
   0.321    0.137    0.403 

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: 351
Number of extensions: 16
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: 406
Length of database: 351
Length adjustment: 30
Effective length of query: 376
Effective length of database: 321
Effective search space:   120696
Effective search space used:   120696
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 (21.8 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