Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 122 bits (307), Expect = 9e-33 Identities = 95/318 (29%), Positives = 150/318 (47%), Gaps = 20/318 (6%) Query: 6 LPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSV 65 L L++ IG+FV P F + + + + +IA M +I+SG IDLSV Sbjct: 26 LLLLVAIGIFVANSFAS----PYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLSV 81 Query: 66 GSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMF 125 S+IA + + G+ + L +G GAF G+L+ + +P+ ++T+ M Sbjct: 82 ASIIALASTAMGAAV-QMGVGTPGLVLIGLGVGLLCGAFNGVLVTRMGLPSIVVTIGTMS 140 Query: 126 FLRGVSYLVSEESIPINHPIYDTLSSLAWKIPG--GGRLSAMGLLMLAVVVIGIFLAHRT 183 RG+SY+V + +P S +W G +S +L + VI L H+T Sbjct: 141 LFRGISYIVLGDQAFRGYP-----ESFSWFGQGYVWWVISFELVLFAIIAVIYAMLLHKT 195 Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGV 243 FG VYAIG NAT A GI + +++L+ ++ +A I + + +G Sbjct: 196 NFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGW 255 Query: 244 ELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQ---TYINFDGTLSSWWTKIAIGIL 300 EL+ + VV+GG + GG GT+LG + + GL+ +N G + S I IG L Sbjct: 256 ELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMS----IVIGAL 311 Query: 301 LFIFIALQRGLTVLWENR 318 L IAL R L +W R Sbjct: 312 LIGVIALPR-LWSMWRAR 328 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: 367 Number of extensions: 27 Number of successful extensions: 4 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: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 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