Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate Pf1N1B4_594 Glucose ABC transport system, inner membrane component 2
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_594 Length = 281 Score = 291 bits (746), Expect = 9e-84 Identities = 141/286 (49%), Positives = 198/286 (69%), Gaps = 11/286 (3%) Query: 20 KPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWV 79 KP + SR I +Y TL++ A YL+PL VM++TS K +IR GN+ + P I W+ Sbjct: 7 KPGISFSR--IAIYATLLLAAAIYLIPLVVMLLTSFKSPEDIRTGNLLSLPQVIDGIGWI 64 Query: 80 KAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILI 139 KAW D + FWNSV+ITVP+V+IS I ++NGY L+ WRF+G+ LFF +L+ Sbjct: 65 KAW---------DSVGSYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLL 115 Query: 140 VGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKA 199 G F+P+Q ++ P L ++G+ T TGL++VH ++G+ TL FRNY+ +P+ L KA Sbjct: 116 FGCFLPFQTVLLPASFTLGKIGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKA 175 Query: 200 ARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNI 259 AR+DGAGF+TI++KI+LPMS+PI +V +I Q T IWNDFLFGVVF + P+TV LNN+ Sbjct: 176 ARLDGAGFFTIFWKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNL 235 Query: 260 VNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 VN+ G KEYNV+MAA ++ GL L VY +G+ F+RG+ +GAVKG Sbjct: 236 VNTSTGAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 Lambda K H 0.329 0.145 0.450 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: 300 Number of extensions: 10 Number of successful extensions: 2 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: 305 Length of database: 281 Length adjustment: 26 Effective length of query: 279 Effective length of database: 255 Effective search space: 71145 Effective search space used: 71145 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: 48 (23.1 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