Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 143 bits (361), Expect = 5e-39 Identities = 96/310 (30%), Positives = 164/310 (52%), Gaps = 17/310 (5%) Query: 8 LMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGS 67 ++I +F++G+ P F + N++ +A LG++A+G+TFV++SG +DLSVGS Sbjct: 18 ILIAFALFIIGFTIAN---PKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGS 74 Query: 68 VIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFL 127 +++F+ + + + G P LA P + M GA +G L+ LK+ + I+TL + + Sbjct: 75 MMSFSTIVVLDLHDKLG--PTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSAI 132 Query: 128 RGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVV----VIGIFLAHRT 183 G++ S N I D + + I G G + + +L + ++GI LA +T Sbjct: 133 HGLTLTYSGGK---NMDIADKEGTW-FAIFGQGNILGIQTPILIFIALAALLGIILA-KT 187 Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGV 243 FG +VYA+GGN T+A GI Y++S AG++ + + G G+ Sbjct: 188 PFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGL 247 Query: 244 ELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQT---YINFDGTLSSWWTKIAIGIL 300 EL+ +A+V++GG L GG GT+ T+ GV I G IQ + D ++ T I I + Sbjct: 248 ELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILA 307 Query: 301 LFIFIALQRG 310 +++ IA +RG Sbjct: 308 VWLDIAAKRG 317 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: 293 Number of extensions: 17 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: 324 Length adjustment: 28 Effective length of query: 303 Effective length of database: 296 Effective search space: 89688 Effective search space used: 89688 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: 48 (23.1 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