Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 3607492 Dshi_0905 protein of unknown function UPF0126 (RefSeq)
Query= reanno::ANA3:7023996 (213 letters) >FitnessBrowser__Dino:3607492 Length = 209 Score = 129 bits (323), Expect = 5e-35 Identities = 64/166 (38%), Positives = 102/166 (61%), Gaps = 4/166 (2%) Query: 4 AQFIGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWV 63 A + L ++ A + A+ A R+ D FG V++ TA+GGGTLRD+L+G +P+ W+ Sbjct: 6 APLVVALTVLATAVMAASAAIQAVRQGFDPFGAVVLAVVTAVGGGTLRDILIGRFPVFWI 65 Query: 64 ENVHYLLAIAFASLLTVAIAPVMRYLS----KLFLAIDALGLAVFSIVGAQKTLMLGFSP 119 E++ Y+ +L++ A MR +L L +DA+GLA+F+++G Q L G SP Sbjct: 66 EDLTYIATAVPVALVSYMAARSMRAGGGRRLRLLLYLDAVGLALFTLIGLQIALGAGVSP 125 Query: 120 TIAVVMGLVTGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYI 165 IA+++G TG+ GG+IRD+LC P + K++LYA ISL +Y+ Sbjct: 126 VIAIILGCTTGIAGGMIRDVLCGLQPSVLKEDLYATISLAGGAVYV 171 Score = 45.1 bits (105), Expect = 1e-09 Identities = 24/64 (37%), Positives = 38/64 (59%) Query: 89 LSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIF 148 L+ L +A+ L AV + A + + GF P AVV+ +VT V GG +RDIL + P+ + Sbjct: 5 LAPLVVALTVLATAVMAASAAIQAVRQGFDPFGAVVLAVVTAVGGGTLRDILIGRFPVFW 64 Query: 149 KKEL 152 ++L Sbjct: 65 IEDL 68 Lambda K H 0.330 0.143 0.438 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: 144 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 213 Length of database: 209 Length adjustment: 21 Effective length of query: 192 Effective length of database: 188 Effective search space: 36096 Effective search space used: 36096 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