GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Synechococcus elongatus PCC 7942

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= SwissProt::P17328
         (400 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1406 Synpcc7942_1406 ATPase
          Length = 368

 Score =  157 bits (398), Expect = 4e-43
 Identities = 92/229 (40%), Positives = 134/229 (58%), Gaps = 9/229 (3%)

Query: 38  TGLSLGVKD-ASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKIS 96
           +G SL   D  S  +E GEI  ++G SG GK+T++R++        G + + G  +A   
Sbjct: 17  SGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQ 76

Query: 97  DAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGM-ELAGIAAQERREKALDALRQVGLE 155
            +   E R   + MVFQ +AL PH+TVLDN  FG+ +  G AA  R+  AL     VGLE
Sbjct: 77  RSLPPETR--SVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQALAL-----VGLE 129

Query: 156 NYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQ 215
                YP ELSGG +QRV LARALA  P ++L+DE  S LD  +R  ++ EL  +  + Q
Sbjct: 130 GLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQ 189

Query: 216 RTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
            T + ++HD +EA+ I DR+A+M+ G   Q+G P+E+  +PA+ +V  F
Sbjct: 190 ATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEF 238


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: 327
Number of extensions: 16
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: 368
Length adjustment: 30
Effective length of query: 370
Effective length of database: 338
Effective search space:   125060
Effective search space used:   125060
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 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