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.
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:
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