Align putative transporter, required for L-alanine utilization (characterized)
to candidate GFF1599 Psest_1636 Predicted membrane protein
Query= reanno::MR1:202450 (213 letters) >FitnessBrowser__psRCH2:GFF1599 Length = 208 Score = 182 bits (462), Expect = 4e-51 Identities = 81/199 (40%), Positives = 134/199 (67%) Query: 5 QFIGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLVWVE 64 + + ++LI I AEAM+GA+ R+ MDLFG+ ++G TA+GGGT RD+LLG+YP+ W+ Sbjct: 2 ELLHTIYLIAITAEAMSGAIMGMRRGMDLFGICLLGTVTALGGGTARDVLLGHYPVGWIA 61 Query: 65 NVHYLIAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVV 124 + YL A+++T IA + +L +FL +D LGL F+++G + +G P+I V+ Sbjct: 62 HPEYLTFTIGAAIVTGFIARHLHHLRMVFLLVDGLGLVAFTVIGCDVAMGMGAHPSIVVL 121 Query: 125 MGLVTGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLEEWINLVICLTL 184 G++TG+FGG++RD+LCNQVP++ ++ELYA ++LFT Y+ + ++ + + L Sbjct: 122 AGVITGIFGGLMRDVLCNQVPMVLQRELYATVALFTGVFYVGMLWLEINTTLATLAALGS 181 Query: 185 GFSLRMLALRYHWSMPTFD 203 GF R+LA+ +HW +P F+ Sbjct: 182 GFLFRVLAMTFHWKLPDFN 200 Lambda K H 0.330 0.143 0.436 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: 155 Number of extensions: 9 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: 213 Length of database: 208 Length adjustment: 21 Effective length of query: 192 Effective length of database: 187 Effective search space: 35904 Effective search space used: 35904 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: 45 (21.9 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