Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate 3608831 Dshi_2223 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__Dino:3608831 Length = 295 Score = 100 bits (250), Expect = 2e-26 Identities = 75/255 (29%), Positives = 123/255 (48%), Gaps = 42/255 (16%) Query: 17 GAWMTLKLAFLALALSLALG-LIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLILLIFY 75 G M L + AL L G IAA ++++ +WL YT+++R +PD+ L + Sbjct: 34 GTVMLLLVVTAPAALFLGFGGAIAARSQIAPLRWL---GKGYTSMVRGIPDIAFFLFVPI 90 Query: 76 SLQLWLNDLSEVF-----------GWDYF-----------------EIDPFTAGVITLGF 107 +L L L + G D+ E FT VI Sbjct: 91 ALDQGLEYLRHHWKCPDWTQAVRQGNDFVVCAEAKLPLSTSPQWVHETYGFTLAVIAFAV 150 Query: 108 IYGAYFTENFRGAILSVPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLL 167 ++GA+ GA+ +VP Q+E A AYG++R Q F +L PQ+ +ALPGL N W +L+ Sbjct: 151 VFGAFAANVLYGAMTAVPRAQIETAEAYGMTRRQAFWRILVPQMWVYALPGLSNLWQILV 210 Query: 168 KSTALVSIIGLSDLVKAAQNAG-----KTTNEP-----LYFLILAGLMYLVITTLSNRVL 217 K+T L+ ++G+ D+V A+ G + ++ P L++ + + YL +T++S R+ Sbjct: 211 KATPLLFLLGIEDIVYWARELGGVQSARFSDYPHGDWRLWYFLGLLVFYLALTSVSERIF 270 Query: 218 KRLERRYNLGIKGMA 232 RL +R + G MA Sbjct: 271 ARLMQRLSHGQATMA 285 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: 177 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: 233 Length of database: 295 Length adjustment: 25 Effective length of query: 208 Effective length of database: 270 Effective search space: 56160 Effective search space used: 56160 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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