Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate PfGW456L13_385 Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3433 (232 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_385 Length = 236 Score = 192 bits (487), Expect = 6e-54 Identities = 98/216 (45%), Positives = 142/216 (65%), Gaps = 1/216 (0%) Query: 15 YLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQLFLI 74 ++ GL TL LL+ S+FFG + ++PL + RVS V +TY+ RGTP+ +QL + Sbjct: 19 HITGLAMTLWLLSASIFFGFVMSIPLSIARVSTNVWVRWPVQFYTYLFRGTPLYIQLLIC 78 Query: 75 YYGLAQFEAVR-ESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKA 133 Y G+ AVR + L + A C LAFA+NT AYT EI AG++R+ +GE+EAAKA Sbjct: 79 YTGIYSLAAVRAQPVLDAFFRDAMNCTILAFALNTCAYTTEIFAGAIRSMAHGEVEAAKA 138 Query: 134 MGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQFYL 193 G++ K+Y +++PSALRR+LP YSNEVI+ML +T++A T+ DI AR N+ +L Sbjct: 139 YGLTGWKLYTYVIMPSALRRSLPYYSNEVILMLHSTTVAFTATIPDILKVARDANSATFL 198 Query: 194 PFEAYITAGVFYLCLTFILVRLFKMAEHRWLGYLAP 229 F+++ A + YL +TF LV LF++AE RWL +L P Sbjct: 199 TFQSFGIAALIYLAVTFSLVGLFRLAERRWLSFLGP 234 Lambda K H 0.330 0.140 0.427 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: 156 Number of extensions: 6 Number of successful extensions: 2 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: 232 Length of database: 236 Length adjustment: 23 Effective length of query: 209 Effective length of database: 213 Effective search space: 44517 Effective search space used: 44517 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 (21.9 bits) S2: 46 (22.3 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