Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_010530733.1 ON01_RS09150 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000224785.1:WP_010530733.1 Length = 355 Score = 162 bits (411), Expect = 1e-44 Identities = 92/238 (38%), Positives = 142/238 (59%), Gaps = 5/238 (2%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 ++ +V KTY G + + LKI++GE + L+GPSGCGK+T M I L + G I Sbjct: 2 IQFSDVKKTYPDGTK-AINDFSLKINEGELVTLIGPSGCGKTTTMKMINRLIEPTAGTIY 60 Query: 64 VDDADISGMSPKDR--DIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121 ++ +I+ + + +I V Q AL+P M++ +NIA +++K EI E + + Sbjct: 61 INGTNINDYNIHELRWNIGYVLQQIALFPHMTIEENIAVVPEMKKWKRKEIRERSEELLE 120 Query: 122 LLQIEH--LLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179 ++ + + R+P +LSGG+QQRV + RALA P I L DEP S LD R +++ ++K Sbjct: 121 MVGLNSSTYMHRRPSELSGGEQQRVGVIRALAADPDIILMDEPFSALDPISREQLQHDIK 180 Query: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIG 237 +HQ ++ T V+VTHD EA+ LGDKV +MK+G I Q TP+ + +P FV FIG Sbjct: 181 KLHQEIRKTIVFVTHDIDEALALGDKVCLMKEGRIIQVDTPQQLVLHPETTFVKDFIG 238 Lambda K H 0.319 0.138 0.393 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: 306 Number of extensions: 12 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: 386 Length of database: 355 Length adjustment: 30 Effective length of query: 356 Effective length of database: 325 Effective search space: 115700 Effective search space used: 115700 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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