Align putative transporter, required for L-alanine utilization (characterized)
to candidate WP_086508172.1 BZY95_RS01150 trimeric intracellular cation channel family protein
Query= reanno::MR1:202450 (213 letters) >NCBI__GCF_002151265.1:WP_086508172.1 Length = 258 Score = 138 bits (347), Expect = 1e-37 Identities = 71/192 (36%), Positives = 118/192 (61%), Gaps = 1/192 (0%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLVWVENVHYLIA 71 + G++ A++G + A R +MD FG++++ T IGGGTLRD++LG P+ WV + YL Sbjct: 10 MAGVVVFALSGVILACRSRMDPFGMLVLAAVTGIGGGTLRDLVLGVRPVFWVADPTYLWV 69 Query: 72 IAFASLLTVAIAPVMRYLSKLFLAI-DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130 I L++ + LS+ FL I DA GLA+F+++GA K L L +AV+MGL+TG Sbjct: 70 ILATVGLSIVGFHYIHRLSRSFLPIADAFGLALFTVIGAHKALQLEAPGVVAVLMGLLTG 129 Query: 131 VFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLEEWINLVICLTLGFSLRM 190 V GG++RD+L +VP++ ++E+YA S+ Y+ L A + + + + L + LR+ Sbjct: 130 VAGGMVRDVLARRVPMVLRQEVYATASIAGGITYVGLGALGVPVGVAIGLALAVTLGLRL 189 Query: 191 LALRYHWSMPTF 202 A+ + ++P F Sbjct: 190 AAIHWQLTLPVF 201 Score = 35.8 bits (81), Expect = 7e-07 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 1/78 (1%) Query: 89 LSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIF 148 ++ L +D G+ VF++ G P +V+ VTG+ GG +RD++ P+ + Sbjct: 1 MTALVYWLDMAGVVVFALSGVILACRSRMDPFGMLVLAAVTGIGGGTLRDLVLGVRPVFW 60 Query: 149 KKE-LYAVISLFTAGLYI 165 + Y + L T GL I Sbjct: 61 VADPTYLWVILATVGLSI 78 Score = 31.6 bits (70), Expect = 1e-05 Identities = 32/131 (24%), Positives = 55/131 (41%), Gaps = 16/131 (12%) Query: 6 FIGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLVWVEN 65 F+ + G+ + GA A + + V++G T + GG +RD+L P+V + Sbjct: 91 FLPIADAFGLALFTVIGAHKALQLEAPGVVAVLMGLLTGVAGGMVRDVLARRVPMVLRQE 150 Query: 66 VHYLIAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVM 125 V+ T +IA + Y + + ALG+ V +G + LG A+ Sbjct: 151 VY----------ATASIAGGITY-----VGLGALGVPVGVAIGLALAVTLGLR-LAAIHW 194 Query: 126 GLVTGVFGGVI 136 L VF V+ Sbjct: 195 QLTLPVFAWVV 205 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: 195 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 213 Length of database: 258 Length adjustment: 23 Effective length of query: 190 Effective length of database: 235 Effective search space: 44650 Effective search space used: 44650 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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