GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Escherichia coli BW25113

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 16237 b2129 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= CharProtDB::CH_001555
         (400 letters)



>lcl|FitnessBrowser__Keio:16237 b2129 predicted transporter subunit:
           ATP-binding component of ABC superfamily (NCBI)
          Length = 308

 Score =  181 bits (458), Expect = 3e-50
 Identities = 100/249 (40%), Positives = 147/249 (59%), Gaps = 9/249 (3%)

Query: 39  GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDA 98
           G    V D +L  +EG   V++G SGSGKST ++++NRL+E   G++   G +I  +   
Sbjct: 12  GAQKAVNDLNLNFQEGSFSVLIGTSGSGKSTTLKMINRLVEHDSGEIRFAGEEIRSLPVL 71

Query: 99  ELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLE-NY 157
           ELR    +++    QS  L PH +V  N A   +L   +     ++  + +  +GLE N 
Sbjct: 72  ELR----RRMGYAIQSIGLFPHWSVAQNIATVPQLQKWSRARIDDRIDELMALLGLESNL 127

Query: 158 AHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRT 217
              YP +LSGG +QRVG+ARALA +P +LLMDE F ALDP+ R  +Q E+ ++     RT
Sbjct: 128 RERYPHQLSGGQQQRVGVARALAADPQVLLMDEPFGALDPVTRGALQQEMTRIHRLLGRT 187

Query: 218 IVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF----RGVDISQV 273
           IV ++HD+DEA+R+ + + +M +GEVVQ G P  +L  PAND+VR FF     GV +  +
Sbjct: 188 IVLVTHDIDEALRLAEHLVLMDHGEVVQQGNPLTMLTRPANDFVRQFFGRSELGVRLLSL 247

Query: 274 FSAKDIARR 282
            S  D  RR
Sbjct: 248 RSVADYVRR 256


Lambda     K      H
   0.319    0.137    0.378 

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: 295
Number of extensions: 8
Number of successful extensions: 3
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: 400
Length of database: 308
Length adjustment: 29
Effective length of query: 371
Effective length of database: 279
Effective search space:   103509
Effective search space used:   103509
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: 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 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