GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pseudomonas stutzeri RCH2

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__psRCH2:GFF3591
          Length = 369

 Score =  221 bits (562), Expect = 3e-62
 Identities = 124/307 (40%), Positives = 186/307 (60%), Gaps = 6/307 (1%)

Query: 8   GVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTV 66
           G++K+Y G+  ++ ++NLDI++GE +  +GPSG GK+T L M+AG E  T G + +DG  
Sbjct: 15  GIQKSYDGESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRA 74

Query: 67  VNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQY 126
           +N+VPP +R + MVFQ+YAL+PHMTV EN++F L +   ++ +I   V+ A   +QL  +
Sbjct: 75  INNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEGF 134

Query: 127 LDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPES 186
            +R P  LSGGQ+QRVA+ R++V +P++ L DEPL  LD  LR   ++EI  L E +   
Sbjct: 135 RNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERL-GV 193

Query: 187 TMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGK 246
           T+VYVTHDQ EA+T++ R+ V   G I Q+  P  LYEKP N FVA F+G  + N LP  
Sbjct: 194 TVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLG--ENNRLPAH 251

Query: 247 IIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMV--EAAPGGDYVFEGKVA 304
           ++     +       G  V     +    G  V++ +RPE ++   A+      F G+VA
Sbjct: 252 LLDRRGDSCTVKLGRGETVEALAVNVGAAGTPVSLSIRPERVLLNGASANCPNRFTGRVA 311

Query: 305 ITEALGE 311
               LG+
Sbjct: 312 EFIYLGD 318


Lambda     K      H
   0.316    0.135    0.379 

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: 370
Number of extensions: 17
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: 373
Length of database: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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