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_004118886.1 RHSP_RS15710 sugar ABC transporter permease YjfF

Query= SwissProt::P37772
         (331 letters)



>NCBI__GCF_000359745.1:WP_004118886.1
          Length = 322

 Score =  385 bits (990), Expect = e-112
 Identities = 199/311 (63%), Positives = 239/311 (76%)

Query: 1   MIKRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGG 60
           M  + LPL+ TI +F+L Y  C+TQ+P   STRV+ N+LTDNAFLGI AVGMTFVI+SGG
Sbjct: 1   MNSKYLPLLATIVIFILAYAGCVTQYPNMLSTRVVGNLLTDNAFLGIAAVGMTFVIISGG 60

Query: 61  IDLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIIT 120
           IDLS+GSVIAFTGVFLA V+ D  + PL+AF LVLV+   FGA MG +I  L +P FI+T
Sbjct: 61  IDLSIGSVIAFTGVFLAIVLRDTTIHPLIAFTLVLVLTTIFGAGMGAIIHYLSMPPFIVT 120

Query: 121 LAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLA 180
           LAGMF  RG+++++S +SIPI H  Y  L+ L W +PGGGRL+ +G +ML V   GI LA
Sbjct: 121 LAGMFLARGIAFVLSIDSIPIEHGFYSQLNDLYWLMPGGGRLTLIGGIMLLVFAGGIVLA 180

Query: 181 HRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAG 240
            RTRFG  VYA+GG   +A LMG+    TTI+IY LS  LA L+GIVFSIYT AGY+LA 
Sbjct: 181 QRTRFGANVYALGGGVQTAELMGVPVGRTTIQIYALSGFLAGLSGIVFSIYTSAGYSLAT 240

Query: 241 VGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGIL 300
           VGVELDAIA+VVIGGTLL+GG G V GTL G+ IQGLIQTYI FDGTLSSWWTKI IG+L
Sbjct: 241 VGVELDAIAAVVIGGTLLTGGAGFVGGTLIGILIQGLIQTYITFDGTLSSWWTKILIGLL 300

Query: 301 LFIFIALQRGL 311
           LF FI +Q+GL
Sbjct: 301 LFAFILMQKGL 311


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: 447
Number of extensions: 20
Number of successful extensions: 1
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: 322
Length adjustment: 28
Effective length of query: 303
Effective length of database: 294
Effective search space:    89082
Effective search space used:    89082
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: 48 (23.1 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