GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Shewanella oneidensis MR-1

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 200225 SO1042 amino acid ABC transporter, ATP-binding protein (NCBI ptt file)

Query= CharProtDB::CH_001555
         (400 letters)



>lcl|FitnessBrowser__MR1:200225 SO1042 amino acid ABC transporter,
           ATP-binding protein (NCBI ptt file)
          Length = 241

 Score =  154 bits (389), Expect = 3e-42
 Identities = 90/219 (41%), Positives = 134/219 (61%), Gaps = 4/219 (1%)

Query: 51  IEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAM 110
           I +GE+  ++G SGSGKST +R +N L  PT+G + I+G  I    DA + ++R+K + M
Sbjct: 24  IRQGEVVSVIGPSGSGKSTFLRCINLLENPTQGDIEIEGQSITA-KDACVDKLRQK-VGM 81

Query: 111 VFQSFALMPHMTVLDN-TAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGM 169
           VFQ+F L PH TVL N T   + L  +   E   KAL  L QVGL++ A++YP  LSGG 
Sbjct: 82  VFQNFNLFPHKTVLQNITLAPVSLKLMTQAEADNKALALLTQVGLQDKANAYPSSLSGGQ 141

Query: 170 RQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAM 229
           +QRV +ARALA+ PD++L DE  SALDP +  ++ D ++K  A+   T+V ++H++  A 
Sbjct: 142 KQRVAIARALAMEPDLMLFDEPTSALDPEMVGDVLD-VMKDLAQKGMTMVIVTHEMGFAR 200

Query: 230 RIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268
            + DR+  M  G VV+   P+E+   P     ++F   V
Sbjct: 201 DVSDRVIFMDGGYVVESNIPEELFTRPKEARTQSFLSKV 239


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: 222
Number of extensions: 15
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: 400
Length of database: 241
Length adjustment: 27
Effective length of query: 373
Effective length of database: 214
Effective search space:    79822
Effective search space used:    79822
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: 48 (23.1 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