Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_073040495.1 BUB04_RS13795 ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3433 (232 letters) >NCBI__GCF_900129305.1:WP_073040495.1 Length = 333 Score = 118 bits (295), Expect = 2e-31 Identities = 71/217 (32%), Positives = 117/217 (53%), Gaps = 16/217 (7%) Query: 14 LYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQLFL 73 + L GL TLK+ +S+FFG+L L GL R+S P + SA + +IRG+P+LVQ+F+ Sbjct: 121 ILLQGLWLTLKVSLISIFFGILIGLIAGLARISDNPALKWSAITYIELIRGSPLLVQIFI 180 Query: 74 IYYGL--------AQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPN 125 Y+ L A+ + LW ++S A+ AY AEI+ +++ Sbjct: 181 WYFVLGTVINTLLAKNGMSQLPPLWYGVAS--------LAVFAGAYVAEIVRAGIQSIHR 232 Query: 126 GEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAAR 185 G++EAA+++GM+ + + ++LP A RR LP + + I +++ +SL I+ + ++T A R Sbjct: 233 GQMEAARSLGMTYPQAMRHVILPQAFRRILPPLAGQFISLIKDSSLLGIIAIRELTKATR 292 Query: 186 TVNAQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHR 222 V PFE + + YL LTF L + E R Sbjct: 293 EVVTTSLQPFELWFVCALLYLVLTFGLSMFVQYLERR 329 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: 169 Number of extensions: 9 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: 333 Length adjustment: 25 Effective length of query: 207 Effective length of database: 308 Effective search space: 63756 Effective search space used: 63756 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: 47 (22.7 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