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.
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