Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 142 bits (358), Expect = 7e-39 Identities = 89/237 (37%), Positives = 128/237 (54%), Gaps = 21/237 (8%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 + + + K Y VL VSL +G ++L+GASG+GK+T+L+ IN L + D G I ++ Sbjct: 2 ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 G + + + LR R+ VFQ L+ HM+V EN+ + PR + V Sbjct: 62 GRDVAAQP------------VAELRRRIGYVFQGIGLFPHMSVAENVALVPR-LQGVPRE 108 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 E R LD V LP+ A++ PA LSGGQ QRV ARALA P I+L DEP ALDP Sbjct: 109 ERAARVAELLDLVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPV 168 Query: 207 LVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDARILDQP 262 E+ + L E G T L+VTH+M A ++ +V+ + +GR+ + DQP Sbjct: 169 TRDELGAAYRALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRI-------LADQP 218 Lambda K H 0.319 0.133 0.372 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: 178 Number of extensions: 7 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: 276 Length of database: 252 Length adjustment: 25 Effective length of query: 251 Effective length of database: 227 Effective search space: 56977 Effective search space used: 56977 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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