Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_004095864.1 M988_RS12735 arginine ABC transporter permease ArtM
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_001655005.1:WP_004095864.1 Length = 222 Score = 151 bits (382), Expect = 9e-42 Identities = 82/220 (37%), Positives = 138/220 (62%), Gaps = 3/220 (1%) Query: 8 IWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPM 67 ++E +P GL T+L L +SLL L+ AL ++ + ++ Y + GTP+ Sbjct: 1 MFEYIPDIIQGLPTSLSLTIISLLVALVLALLFTIVLTLRPVVLTQLVQGYITLFTGTPL 60 Query: 68 LVQLFLIYYGLAQFEAVRES-FLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNG 126 LVQ+FLIYYG QF+ ++++ +LW LS CA +A A+N++AYT ++ G+++A P+G Sbjct: 61 LVQIFLIYYGPGQFDWIKQTPWLWNMLSQPWLCAMVALALNSAAYTTQLFYGAVKAIPSG 120 Query: 127 EIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAART 186 + ++ +A+GMSR + RILLP A +RAL YSNEV+++ ++TSLA +TL+++ G ++ Sbjct: 121 QWQSCEALGMSRSQTL-RILLPFAFKRALSSYSNEVVLIFKSTSLAYTITLMEVMGYSQQ 179 Query: 187 VNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGY 226 + + Y + AGV YLC+ +L + +M E R L + Sbjct: 180 MYGRTY-DVMVFGAAGVIYLCVNGLLTLIMRMVERRALAF 218 Lambda K H 0.329 0.139 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: 153 Number of extensions: 9 Number of successful extensions: 4 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: 222 Length adjustment: 22 Effective length of query: 210 Effective length of database: 200 Effective search space: 42000 Effective search space used: 42000 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