Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_067073689.1 MCUHO_RS04035 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >NCBI__GCF_001602375.1:WP_067073689.1 Length = 228 Score = 94.0 bits (232), Expect = 2e-24 Identities = 66/216 (30%), Positives = 110/216 (50%), Gaps = 16/216 (7%) Query: 9 ILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILLI 68 ++ G+ +TLQL S + LG+ R ++WL Y +I+G P L+L+ ++ Sbjct: 15 LMQGLIVTLQLIACSAPFGLALGIAVAVGRQYGHPVISWLCKTYVFLIKGTPLLLLLFIL 74 Query: 69 FYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIF--GAYLSETFRGAFMAIPKGQAE 126 ++G P G I A + +GFI GAY +E RGA ++I +GQ Sbjct: 75 YFG--------LPSIG----ITFTAFVASV--VGFILCNGAYNAEYIRGALISIKEGQMV 120 Query: 127 AGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAAD 186 A A GM+ +Q V++PQ + AIPG +N ++ L K ++L ++ + ++ K A Sbjct: 121 AAQALGMTRWQAIRNVILPQALCRAIPGLSNEFIYLIKYSSLAYMITVIELSGAGKLVAT 180 Query: 187 ATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSV 222 F AV +YLV+ S++ +A+ LEKR +V Sbjct: 181 KYFTYTESFAAVGIVYLVLVSITTIAVTILEKRVAV 216 Lambda K H 0.329 0.144 0.428 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: 143 Number of extensions: 11 Number of successful extensions: 3 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: 229 Length of database: 228 Length adjustment: 23 Effective length of query: 206 Effective length of database: 205 Effective search space: 42230 Effective search space used: 42230 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