Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate CA265_RS15435 CA265_RS15435 hypothetical protein
Query= reanno::ANA3:7023996 (213 letters) >FitnessBrowser__Pedo557:CA265_RS15435 Length = 204 Score = 190 bits (482), Expect = 2e-53 Identities = 90/197 (45%), Positives = 133/197 (67%) Query: 9 LLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHY 68 +L++I I AEAMT AL+AGR+ MD GV II TA+GGGT+R++L G+YP+ WVE+ Y Sbjct: 4 ILYIIAITAEAMTAALSAGRRDMDWVGVCIIAWVTALGGGTVRNVLFGHYPMSWVEHPEY 63 Query: 69 LLAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLV 128 L+ A A+LL IA +M L KLFL +DALGL VF+I+G Q + I + G++ Sbjct: 64 LVITAVAALLAAFIASIMTKLKKLFLYLDALGLVVFTIIGCQVAQQIHLPYLIVLFSGMI 123 Query: 129 TGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGFSL 188 TG GGV+RD+LCN+VP +F+KE+YA ++ T +YI + + +E + + +G +L Sbjct: 124 TGCAGGVLRDVLCNEVPFLFRKEIYASAAIVTGAVYIGIEHFHGSEMLATITAAIIGLTL 183 Query: 189 RMLALRYHWSMPTFDYQ 205 R+L++R+ W MP F Y+ Sbjct: 184 RLLSIRFEWHMPKFVYR 200 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: 148 Number of extensions: 3 Number of successful extensions: 1 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: 204 Length adjustment: 21 Effective length of query: 192 Effective length of database: 183 Effective search space: 35136 Effective search space used: 35136 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