GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Rhizobium freirei PRF 81

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate WP_004111334.1 RHSP_RS07045 ABC transporter permease

Query= SwissProt::P37772
         (331 letters)



>NCBI__GCF_000359745.1:WP_004111334.1
          Length = 326

 Score =  169 bits (428), Expect = 9e-47
 Identities = 110/280 (39%), Positives = 155/280 (55%), Gaps = 4/280 (1%)

Query: 29  FASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVIGDFGLSPL 88
           F S R   NIL     LGI+AVGMTFVIL GGIDLSVGSV+A   + +       GL  +
Sbjct: 44  FLSLRNGLNILDQITVLGIMAVGMTFVILIGGIDLSVGSVLALAMMVMGWTANIAGLPLV 103

Query: 89  LAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDT 148
               + LV     G  +GLL+   ++PAFI TLA M   RGV+ ++++    +  P +  
Sbjct: 104 AGVAVALVASALSGLIVGLLVTLFRVPAFIATLAMMSAARGVANMITDGQQIVGFPDWFM 163

Query: 149 LSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQVYAIGGNATSANLMGISTRS 208
           + ++       G L+A   LMLAVV       H    G  +YA+GGN   A L GI+ + 
Sbjct: 164 MLAIDRHF---GVLTATVFLMLAVVAAAWVFLHFRSEGRMLYAVGGNPEVARLAGINVQL 220

Query: 209 TTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGT 268
            TI +Y+ S  LA LAGIV +    +    +G G ELD IA+VVIGGT LSGG G + GT
Sbjct: 221 VTIAVYVASAVLAGLAGIVLAARLDSVQPSSGFGYELDTIAAVVIGGTSLSGGSGGIGGT 280

Query: 269 LFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIALQ 308
           L GV I G+++  +N    +S +  ++ IGI++ + +  +
Sbjct: 281 LIGVLIIGVLRNGLNL-LNVSPFLQQVIIGIVIVLAVGAE 319


Lambda     K      H
   0.329    0.145    0.428 

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: 354
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: 331
Length of database: 326
Length adjustment: 28
Effective length of query: 303
Effective length of database: 298
Effective search space:    90294
Effective search space used:    90294
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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