GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Pseudomonas fluorescens FW300-N1B4

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Pf1N1B4_2420 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2420
          Length = 392

 Score =  279 bits (714), Expect = 9e-80
 Identities = 144/277 (51%), Positives = 203/277 (73%), Gaps = 4/277 (1%)

Query: 13  IFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVR 72
           IF + P+ A K ++QG+++ +IL+KTG  +GV+ ASL IE+GEI V+MGLSGSGKS+++R
Sbjct: 12  IFSKDPREALKLLDQGMTRNEILKKTGQIVGVEKASLDIEKGEICVLMGLSGSGKSSLLR 71

Query: 73  LLNRLIEPTRGQVLIDG----VDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTA 128
            +N L   +RG++ ++     +DIA  + AEL+ +R K+IAMVFQ FALMP +TV +N +
Sbjct: 72  CINGLNTVSRGKLFVEHEGKQIDIASCTPAELKMMRTKRIAMVFQKFALMPWLTVRENIS 131

Query: 129 FGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLM 188
           FG+E+ G   +ER++   + L  VGL  + +  PDELSGGM+QRVGLARALA++ DILLM
Sbjct: 132 FGLEMQGRPEKERKKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALAMDADILLM 191

Query: 189 DEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGT 248
           DE FSALDPLIR  +QDEL++LQ K  +TIVF+SHDLDEA+++G RIAIM++G ++Q   
Sbjct: 192 DEPFSALDPLIRQGLQDELLELQRKLSKTIVFVSHDLDEALKLGSRIAIMKDGRIIQYSK 251

Query: 249 PDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPN 285
           P+EI+ NPA+DYVRTF    +   V   + + R   N
Sbjct: 252 PEEIVLNPADDYVRTFVAHTNPLNVLCGRSLMRTLDN 288


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: 452
Number of extensions: 15
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: 392
Length adjustment: 31
Effective length of query: 369
Effective length of database: 361
Effective search space:   133209
Effective search space used:   133209
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.

Links

Downloads

Related tools

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