Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 96.3 bits (238), Expect = 7e-25 Identities = 46/135 (34%), Positives = 83/135 (61%) Query: 85 LLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVV 144 L P FV + G IY+ A+ +E+VRG + + +GQ EA+R++G+S ++R V++PQA+ Sbjct: 239 LTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALR 298 Query: 145 RMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYLAIAVVYFILTGAT 204 ++PP+ ++FI ++KNS L ++ DL I+ + + LE + +V+F L A Sbjct: 299 MIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASAI 358 Query: 205 TLVLRRIELRLRAGG 219 +L + R+ R++ GG Sbjct: 359 SLAMNRLNARVQRGG 373 Score = 26.9 bits (58), Expect = 5e-04 Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 7/68 (10%) Query: 22 TVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFILFFGLPQ 81 ++ +T ++L + G+ + + R + + L +V +R PL+VQL LF+ Sbjct: 82 SIALTLLIIVLSTMAGVPIALAR-HSGHMLARTLAGGFVDLVRNVPLVVQL--LFW---- 134 Query: 82 FGILLPAF 89 +G++L AF Sbjct: 135 YGVILMAF 142 Lambda K H 0.328 0.143 0.412 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: 205 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 222 Length of database: 374 Length adjustment: 26 Effective length of query: 196 Effective length of database: 348 Effective search space: 68208 Effective search space used: 68208 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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