Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate SMc02031 SMc02031 permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 159 bits (402), Expect = 1e-43 Identities = 115/323 (35%), Positives = 168/323 (52%), Gaps = 23/323 (7%) Query: 14 VFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAF-- 71 V ++ YL T F + + N+ +AF+ I+AVG TFVIL+GGIDLSV ++ A Sbjct: 37 VLLMAYLAFATS--NFLTLDNLSNVARQSAFVAILAVGQTFVILTGGIDLSVAAIAALSA 94 Query: 72 --TGVFLAKVIGDFGLS-----PLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGM 124 T V L + + FG+ P +A + +++G A GA G LI KIP FI TL M Sbjct: 95 SITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGWLISKFKIPDFIATLGTM 154 Query: 125 FFLRGVSYLVSEE-SIPINHPIYDTLSSLAWKIPGGGRLSAM---GLLMLAVVVIGIFLA 180 RG + LV++ +P + SL W GGG+L + L+ L G ++ Sbjct: 155 TAFRGAALLVTDGLPVPSFNAGRQLPESLIWV--GGGQLFGVPVSALIALLCAAAGWYVL 212 Query: 181 HRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAG 240 T G +YA+GGN +A+ GIS T I Y +S LA +AGI+ + AL Sbjct: 213 RYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRLNSANALMA 272 Query: 241 VGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGIL 300 G EL +IASVVIGGT L GG G V G++ G AI G++ +N +S +W +IA G++ Sbjct: 273 DGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNL-LDVSPFWQRIAQGVV 331 Query: 301 LFIFIALQRGLTVLWENRQSSPV 323 + + + + W R + V Sbjct: 332 IVVVVIFDQ-----WRRRSMTRV 349 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: 315 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 349 Length adjustment: 28 Effective length of query: 303 Effective length of database: 321 Effective search space: 97263 Effective search space used: 97263 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 17 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