Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate AO356_23245 AO356_23245 ABC transporter substrate-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09620 (322 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23245 Length = 336 Score = 319 bits (817), Expect = 7e-92 Identities = 152/308 (49%), Positives = 206/308 (66%), Gaps = 19/308 (6%) Query: 34 PVKFAGLNWESGMLLTDVLQVVLEKGYDCKTDSLPGNSITMENALSSNDIQVFAEEWVGR 93 P+ FA LNWESG L+TD+L+V++EKGY +TD+LPG +IT+E AL++NDIQV EEW GR Sbjct: 29 PIHFADLNWESGSLITDILRVIVEKGYGLQTDTLPGTTITLETALANNDIQVIGEEWAGR 88 Query: 94 SEVWNKAEKAGKVVGVGAPVVGAIEGWYVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAA 153 S VW KAE GKVV +G V GA EGW+VP YV++GD + ++ AP L+++ DL +Y Sbjct: 89 SPVWVKAEAEGKVVALGDTVKGATEGWWVPEYVIKGDPAKGIKPLAPDLRSVEDLARYKH 148 Query: 154 VFKDPEEPSKGRFYNCPAGWTCELDNSEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKR 213 VFKDPE P KGRF N P GWT E+ N + LK+YGL +Y NFR G+G ALDA + S+ +R Sbjct: 149 VFKDPESPDKGRFLNSPIGWTSEVVNKQKLKAYGLSDSYVNFRSGSGAALDAEISSTIRR 208 Query: 214 GEPILFYYWSPTPLMGQVDLVKLEE-------------------KPGVDKSVSIKVGLSK 254 G+PILFYYWSPTPL+G+ LV+L+E KP + + +G+S Sbjct: 209 GKPILFYYWSPTPLLGRFKLVQLQEPPFDAEAWKTLTDADNPNPKPTRSLASKLSIGVSA 268 Query: 255 TFHDEAPELVAVLEKVNLPIDILNQNLGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDA 314 F + PE+ KV+LPI+ LN+ L M+++R + A+ FLK HPEVW AW+ ++ Sbjct: 269 PFQKQYPEIAEFFSKVDLPIEPLNKTLADMSEKRTPPREAAEAFLKAHPEVWQAWLPKEV 328 Query: 315 AKKIDAAL 322 A K+ A L Sbjct: 329 ADKVSAGL 336 Lambda K H 0.314 0.133 0.398 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: 325 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: 322 Length of database: 336 Length adjustment: 28 Effective length of query: 294 Effective length of database: 308 Effective search space: 90552 Effective search space used: 90552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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