Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate HSERO_RS05185 HSERO_RS05185 ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS05185 Length = 340 Score = 286 bits (733), Expect = 4e-82 Identities = 156/305 (51%), Positives = 207/305 (67%), Gaps = 1/305 (0%) Query: 9 MITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSV 68 M+T+ + V+ + + GF S +V+ N+L DNAFL ++A+GMTFVILSGGIDLSVGSV Sbjct: 19 MVTVVLLVVMLVAGALGYDGFLSPQVMLNLLIDNAFLLVVAIGMTFVILSGGIDLSVGSV 78 Query: 69 IAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLR 128 +A T + A ++ ++ PLL VL+MG FGA MG +I K+ AFI+TLAGMF R Sbjct: 79 LALTTMVAAFLLQNWHWHPLLVIVTVLLMGAGFGAAMGAMIHYFKLQAFIVTLAGMFLAR 138 Query: 129 GVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQ 188 G+ YL+S SI I+ P++ TLS ++ G +S ++ L ++ + I++AH TRFG Sbjct: 139 GLCYLISINSITIDDPLFTTLSQTRLEL-AGLFISPSVVIALFMLALAIWMAHCTRFGRA 197 Query: 189 VYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAI 248 VYAIGGN SA LMG+ T + +Y S A +AG++FS Y +GY L GVELDAI Sbjct: 198 VYAIGGNENSALLMGLPVGRTKVLVYAFSGLCAAVAGVLFSFYMLSGYGLHAQGVELDAI 257 Query: 249 ASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIALQ 308 A+VVIGGTLL+GG G V GTL GV I G+IQT I FDGTLSSWWTKI IG LLF+F Q Sbjct: 258 AAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIFIGALLFVFCVAQ 317 Query: 309 RGLTV 313 R +++ Sbjct: 318 RVISL 322 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: 353 Number of extensions: 12 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: 340 Length adjustment: 28 Effective length of query: 303 Effective length of database: 312 Effective search space: 94536 Effective search space used: 94536 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