Align putative transporter, required for L-alanine utilization (characterized)
to candidate 200494 SO1319 conserved hypothetical protein (NCBI ptt file)
Query= reanno::MR1:202450 (213 letters) >FitnessBrowser__MR1:200494 Length = 208 Score = 157 bits (398), Expect = 1e-43 Identities = 78/196 (39%), Positives = 125/196 (63%), Gaps = 1/196 (0%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLVWVENVHYLIA 71 L G A++GALAAGR +MD FGV+++ TA+GGG++RD L+G P+ W+ + +Y+I Sbjct: 10 LCGTAVFALSGALAAGRHRMDPFGVIVLASVTAVGGGSIRDALIGATPVFWIRDPNYIIV 69 Query: 72 IAFASLLTVAIAPVMRYLSKLFLAI-DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130 I + + + R + + L + DALGLA+F+++GA+K L +G S IAVVMGL+TG Sbjct: 70 ILATVVACLLLVRRPRKMPEYVLPVADALGLALFTVIGAEKALNMGLSGMIAVVMGLITG 129 Query: 131 VFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLEEWINLVICLTLGFSLRM 190 V GG+IRD+LC Q+P++ + E+YA S+ Y A + E L + + +R+ Sbjct: 130 VGGGIIRDLLCRQIPMVLRTEIYATASIIGGIGYTVSLACGMGEKTALFLAMASALIIRL 189 Query: 191 LALRYHWSMPTFDYQS 206 A+++H S+P FD ++ Sbjct: 190 CAIKWHLSLPAFDLKT 205 Score = 36.6 bits (83), Expect = 3e-07 Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 4/95 (4%) Query: 97 DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIFKKE---LY 153 D G AVF++ GA P +V+ VT V GG IRD L P+ + ++ + Sbjct: 9 DLCGTAVFALSGALAAGRHRMDPFGVIVLASVTAVGGGSIRDALIGATPVFWIRDPNYII 68 Query: 154 AVISLFTAGLYITLNAYQLEEWINLVICLTLGFSL 188 +++ A L + ++ E++ L + LG +L Sbjct: 69 VILATVVACLLLVRRPRKMPEYV-LPVADALGLAL 102 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: 150 Number of extensions: 7 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: 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