Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate H281DRAFT_05272 H281DRAFT_05272 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_05272 Length = 365 Score = 290 bits (743), Expect = 3e-83 Identities = 157/306 (51%), Positives = 206/306 (67%), Gaps = 1/306 (0%) Query: 4 RNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDL 63 R LP+ +TI +F + + + GF S +V+ ++L DNAFL I+A+GMTFVI+SGGIDL Sbjct: 15 RTLPIAVTILLFCALFGFGSVMYTGFFSWQVLLDLLVDNAFLLIVAIGMTFVIVSGGIDL 74 Query: 64 SVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAG 123 SVGSV+A T + A + + LS + P+VLVMG FGA G LI ++ AFI+TLAG Sbjct: 75 SVGSVVALTTIVEAVLSERYHLSVWVIVPIVLVMGTVFGAVQGALIHFFRLQAFIVTLAG 134 Query: 124 MFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRT 183 MFF RG+ +L++ +SI I P + +S+ I G G ++A L+ ++ I++AH T Sbjct: 135 MFFARGLCFLITTQSITITDPTFHAISAFRLDI-GIGSVTANVLIAFVALLGAIYVAHFT 193 Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGV 243 RFG VYA+GGNA SA LMG+ T I +Y LS + L G VF+ Y +GY L G G+ Sbjct: 194 RFGRNVYAVGGNARSALLMGLPVAHTRIGVYALSGFCSALGGAVFTFYVLSGYGLQGQGM 253 Query: 244 ELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFI 303 ELDAIA+ VIGGTLL+GGVG V+G+LFGV I G IQT I FDGTLSSWWT+I IG LL Sbjct: 254 ELDAIAATVIGGTLLTGGVGYVVGSLFGVGILGTIQTLITFDGTLSSWWTRIVIGALLCA 313 Query: 304 FIALQR 309 F LQR Sbjct: 314 FCLLQR 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: 371 Number of extensions: 24 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: 365 Length adjustment: 29 Effective length of query: 302 Effective length of database: 336 Effective search space: 101472 Effective search space used: 101472 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