Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate WP_068169054.1 HTA01S_RS08130 ABC transporter permease subunit
Query= uniprot:A0A1N7UBU2 (233 letters) >NCBI__GCF_001592305.1:WP_068169054.1 Length = 233 Score = 211 bits (536), Expect = 1e-59 Identities = 107/222 (48%), Positives = 158/222 (71%), Gaps = 6/222 (2%) Query: 14 LAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLILLI 73 + QG +T+ ++ AL ++ LGL AAAKLS +WL +Y+T+IR VPDLV +LL+ Sbjct: 8 ILQGLLVTIGVSLGALIVAALLGLAGAAAKLSHHRWLNWLGDIYSTVIRGVPDLVWMLLL 67 Query: 74 FYSLQLWLNDLSEVFGWDYF-EIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLEAA 132 ++ Q+ +ND++E G+ +I+PF AGV+T+GF+YGAY TE FRGAI+SVP GQ EA Sbjct: 68 YFGGQILVNDIAEALGFRSGPQINPFVAGVLTIGFVYGAYMTETFRGAIMSVPKGQSEAG 127 Query: 133 TAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNA---- 188 A+G+SR+ F ++ PQ++RFALP NNWLVLLK+TALVS+IGL+D+ A+ A Sbjct: 128 WAFGMSRFYTFRRMVLPQMVRFALPSFTNNWLVLLKATALVSVIGLADITNLAKQAGAAA 187 Query: 189 -GKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIK 229 G+ + F+ AGL+YL+IT++S +L+R E+RY++G+K Sbjct: 188 RGQIPGAAIIFMAFAGLLYLLITSISLLLLRRAEKRYSVGVK 229 Lambda K H 0.327 0.141 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: 203 Number of extensions: 8 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: 233 Length of database: 233 Length adjustment: 23 Effective length of query: 210 Effective length of database: 210 Effective search space: 44100 Effective search space used: 44100 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 (21.7 bits) S2: 46 (22.3 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