GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Desulfoscipio geothermicus DSM 3669

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  166 bits (420), Expect = 9e-46
 Identities = 85/246 (34%), Positives = 146/246 (59%), Gaps = 12/246 (4%)

Query: 35  LEKTGLSLG---VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVD 91
           LE   + LG   + D +L ++EGE F+I+G +G+GK+ ++  +  +  P +G +     +
Sbjct: 4   LEHVTVKLGEFQLLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERN 63

Query: 92  IAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQ 151
           +A ++  +      +K+  V+Q +AL PH+TV +N  FG ++  +  +  + K  + +  
Sbjct: 64  LATLAPEQ------RKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAM 117

Query: 152 VGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQ 211
           +G+ +  + +P  LSGG +QR  LARAL I+P+ILL+DE  SALDP  +   Q+EL K+ 
Sbjct: 118 LGIGHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIH 177

Query: 212 AKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDIS 271
              + T + ++HD +EAM + D+I +M  G+++QVGTP EI   P ND+V +F   V I 
Sbjct: 178 QTLKTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASF---VGIE 234

Query: 272 QVFSAK 277
            +F  +
Sbjct: 235 NIFEGQ 240


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: 313
Number of extensions: 19
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: 344
Length adjustment: 30
Effective length of query: 370
Effective length of database: 314
Effective search space:   116180
Effective search space used:   116180
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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