GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Desulfovibrio vulgaris Miyazaki F

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__Miya:8500851
          Length = 354

 Score =  171 bits (433), Expect = 3e-47
 Identities = 96/260 (36%), Positives = 150/260 (57%), Gaps = 7/260 (2%)

Query: 34  ILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIA 93
           + ++ G    V   +L I  GE F ++G SG GK+T +R++    +   G++ +    ++
Sbjct: 9   VTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEIHVGDRLLS 68

Query: 94  KISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVG 153
              +       ++   MVFQ+FA+ PH++V +N AF + +  ++A E   +  +AL    
Sbjct: 69  ARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRTREALHHTS 128

Query: 154 LENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAK 213
           L + A   PD+LSGG +QRV LARALAINPD++L+DE  S+LDP +R EM+ E+  LQ  
Sbjct: 129 LADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRFEIKDLQRT 188

Query: 214 HQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQV 273
              +I++++HD  EAM + DRI +M+NG V QVGTP ++  NPAN +V   F  + +S  
Sbjct: 189 FGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFV---FGFIGLSNF 245

Query: 274 FSAKDIARRTPNGLIRKTPG 293
                    TP GL+R   G
Sbjct: 246 LD----VNLTPEGLVRVNGG 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: 327
Number of extensions: 16
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: 354
Length adjustment: 30
Effective length of query: 370
Effective length of database: 324
Effective search space:   119880
Effective search space used:   119880
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: 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 (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