GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Pseudomonas stutzeri RCH2

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF559 Psest_0564 urea ABC transporter, ATP-binding protein UrtD

Query= uniprot:Q1MCU2
         (292 letters)



>lcl|FitnessBrowser__psRCH2:GFF559 Psest_0564 urea ABC transporter,
           ATP-binding protein UrtD
          Length = 283

 Score =  139 bits (350), Expect = 7e-38
 Identities = 96/260 (36%), Positives = 138/260 (53%), Gaps = 19/260 (7%)

Query: 13  TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72
           T+L +E +++ F G  A+ D S     G++  +IGPNGAGKTT+ + ITG  +PT G   
Sbjct: 41  TILSLEDINVSFDGFKALTDLSLYIGVGELRCIIGPNGAGKTTMMDVITGKTRPTSGSAW 100

Query: 73  FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQH-NKLMKASGYT 131
           F    G+   L R+ +  I  +A + R FQ   +F  L+V ENL +AQ  +K + AS   
Sbjct: 101 F----GETLDLTRMSEVDIA-QAGIGRKFQKPTVFEALSVFENLELAQKTDKSVWASLRA 155

Query: 132 ILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191
            L     G  K    E +E  R       L      PAG L +G ++ LEI   +   P+
Sbjct: 156 KLS----GEQKDRIDEVLETIR-------LGQSRHRPAGLLSHGQKQFLEIGMLLMQSPQ 204

Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251
           LL LDEP AG+   E+     L KS+  +   S++++EHDM  V  I+DHV VL  GQ +
Sbjct: 205 LLLLDEPVAGMTDAETEFTAELFKSLARK--HSLMVVEHDMGFVETIADHVTVLHQGQVL 262

Query: 252 SDGTPDHVKNDPRVIAAYLG 271
           ++G+   V+ D RVI  YLG
Sbjct: 263 AEGSLQQVQADERVIEVYLG 282


Lambda     K      H
   0.318    0.136    0.386 

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: 176
Number of extensions: 8
Number of successful extensions: 4
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: 292
Length of database: 283
Length adjustment: 26
Effective length of query: 266
Effective length of database: 257
Effective search space:    68362
Effective search space used:    68362
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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