GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Shewanella loihica PV-4

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)

Query= SwissProt::P17328
         (400 letters)



>lcl|FitnessBrowser__PV4:5210736 Shew_3164 ABC transporter-related
           protein (RefSeq)
          Length = 241

 Score =  150 bits (378), Expect = 5e-41
 Identities = 94/265 (35%), Positives = 146/265 (55%), Gaps = 28/265 (10%)

Query: 5   LEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64
           +++ NL+K FG++       + KG+ +                  +I  GE+  ++G SG
Sbjct: 2   IKISNLHKYFGDNQ------VLKGIDE------------------SIARGEVVSVIGPSG 37

Query: 65  SGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVL 124
           SGKST +R +N L +PT+G+++IDG  I    DA + ++R+K + MVFQ+F L PH TV 
Sbjct: 38  SGKSTFLRCINLLEQPTQGEIVIDGQSITA-PDACIDKLRQK-VGMVFQNFNLFPHKTVQ 95

Query: 125 DNTAFGMELAGIAAQ-ERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINP 183
            N        G+  Q E   +A+  L QVGL + A AYP  LSGG +QRV +ARALA+ P
Sbjct: 96  QNITLAPVKLGLMTQAEADSEAMRLLDQVGLSDKASAYPASLSGGQKQRVAIARALAMKP 155

Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243
           +++L DE  SALDP +  ++ D ++K  A+   T+V ++H++  A  + DR+  M  G V
Sbjct: 156 ELMLFDEPTSALDPEMVGDVLD-VMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYV 214

Query: 244 VQVGTPDEILNNPANDYVRTFFRGV 268
           V+   P  +   P     + F   V
Sbjct: 215 VESNVPALLFGQPQEPRTQAFLSKV 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: 271
Number of extensions: 14
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 (21.8 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