Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate AO353_29015 AO353_29015 ABC transporter substrate-binding protein
Query= CharProtDB::CH_014295 (260 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29015 Length = 262 Score = 282 bits (722), Expect = 4e-81 Identities = 136/260 (52%), Positives = 185/260 (71%), Gaps = 1/260 (0%) Query: 1 MKKLVLSLSLVLAFSSATAAFAAIPQNI-RIGTDPTYAPFESKNSQGELVGFDIDLAKEL 59 M K++ ++SLV +S A A + R+G DPTY P E KN G L GF +D+A L Sbjct: 1 MNKMIAAVSLVFLTASGLAGAADWSGKVLRLGIDPTYPPLEYKNQDGTLTGFGVDIADAL 60 Query: 60 CKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVA 119 C ++ +C +VE+ D +IP L A+K DAI SS+++T KRQ++IAF+DK+ A +RLV+ Sbjct: 61 CAELHAKCVWVESSWDGMIPGLLARKFDAIASSMTVTPKRQEQIAFSDKVSNAPARLVIK 120 Query: 120 KNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDA 179 + SD+QPTVESLKGKR+GV QG+TQE F W +G+EI+SYQ QD +Y+DL GR+DA Sbjct: 121 RGSDLQPTVESLKGKRIGVEQGSTQEAFAKAVWGKQGVEILSYQNQDQVYADLVVGRLDA 180 Query: 180 AFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEM 239 + Q + AS GFL +PVGKDY+F G ++ + + FGVG G+G+RK D ELRE LNKA A + Sbjct: 181 SLQGSIQASYGFLNKPVGKDYEFAGGTLDNPEFFGVGDGIGVRKSDVELREDLNKALATI 240 Query: 240 RADGTYEKLAKKYFDFDVYG 259 A+GTY K+ KKYFDFD+YG Sbjct: 241 LANGTYAKINKKYFDFDIYG 260 Lambda K H 0.315 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: 239 Number of extensions: 12 Number of successful extensions: 1 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: 260 Length of database: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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