Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 149 bits (377), Expect = 7e-41 Identities = 111/312 (35%), Positives = 163/312 (52%), Gaps = 13/312 (4%) Query: 2 IKRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGI 61 +KR+ IG+ V+ + F S I N+L + IIAVGMT VIL+GGI Sbjct: 31 LKRSTLFYPFIGLLVVCIVMVFAS-DSFLSGANIENVLRQVSINAIIAVGMTCVILTGGI 89 Query: 62 DLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITL 121 DLSVGSV+A G A ++ G++ + A + + +G FGA G + +P I+TL Sbjct: 90 DLSVGSVMALAGTLAAGLMVA-GMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTL 148 Query: 122 AGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRL---SAMGLLMLAVVVIGIF 178 A M RG++ L+ PI+ + D +S G G++ A ++M + VI Sbjct: 149 ATMGIARGLA-LIYTGGYPIDG-LPDWVSFF-----GSGKILGVQAPVVIMAVIYVIAWV 201 Query: 179 LAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYAL 238 L R FG VYAIGGN + L G+ + +Y ++ + A IV + +G Sbjct: 202 LLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPN 261 Query: 239 AGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIG 298 AGVG ELDAIA+VV+GGT +SGG G+++GTL G + G++ +N G I G Sbjct: 262 AGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGG 321 Query: 299 -ILLFIFIALQR 309 ILL I+I+ R Sbjct: 322 IILLAIYISRDR 333 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: 342 Number of extensions: 29 Number of successful extensions: 3 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: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 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