GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Synechococcus elongatus PCC 7942

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= CharProtDB::CH_001555
         (400 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1680 Synpcc7942_1680 Sulphate
           transport system permease protein 1
          Length = 338

 Score =  191 bits (486), Expect = 2e-53
 Identities = 105/266 (39%), Positives = 155/266 (58%), Gaps = 10/266 (3%)

Query: 28  GLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLI 87
           G+   Q+ ++ G    VKD  L +E G +  ++G SGSGKST++RL+  L +P  G++ +
Sbjct: 2   GIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFL 61

Query: 88  DGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALD 147
            G       DA    VR ++I  VFQ +AL  H+TV  N AFG+EL     E+ R +  +
Sbjct: 62  TG------RDATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEE 115

Query: 148 ALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDEL 207
            L  V L      YP +LSGG RQRV LARALA+ P +LL+DE F ALD  +R +++  L
Sbjct: 116 LLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWL 175

Query: 208 VKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRG 267
            KL  +   T VF++HD +EAM + D+I +M +G+V Q+G+P EI +NPA  +V +F   
Sbjct: 176 RKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIGP 235

Query: 268 VDI----SQVFSAKDIARRTPNGLIR 289
           V++    S +F A  +    P   +R
Sbjct: 236 VNVLPNSSHIFQAGGLDTPHPEVFLR 261


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: 339
Number of extensions: 15
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: 400
Length of database: 338
Length adjustment: 30
Effective length of query: 370
Effective length of database: 308
Effective search space:   113960
Effective search space used:   113960
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, the preprint on GapMind for carbon sources, 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