Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 236 bits (601), Expect = 9e-67 Identities = 126/288 (43%), Positives = 181/288 (62%), Gaps = 8/288 (2%) Query: 3 SVTLRNIRKAYDENE----VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58 ++ +RN+ K Y ++ + ++++DIAD EF +GPSGCGK+TL+R IAG E +S G Sbjct: 6 AIEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSDG 65 Query: 59 DLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118 ++ + G VND+ P KR + VFQSYAL+PHM++ N+AFGL++ G + I V Sbjct: 66 EIRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEML 125 Query: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178 ++ + HL RKP +LSGGQ+QRVA+ RA+ KPKV L DEPLS LD LR +M++E R Sbjct: 126 ALVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELKR 185 Query: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238 + E T I+VTHDQ EA+TL+D+I V+SAG + Q+GSP +Y P ++FVA FIG Sbjct: 186 VQKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIGD-- 243 Query: 239 MNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPE 286 +NF+ G ++ + G + PA G KV + RPE Sbjct: 244 INFLPGHIKR-GQQNEKLFVPNGMPVEIPC-PAQGFDGSKVQLAFRPE 289 Lambda K H 0.320 0.135 0.384 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: 350 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: 1 Length of query: 369 Length of database: 361 Length adjustment: 30 Effective length of query: 339 Effective length of database: 331 Effective search space: 112209 Effective search space used: 112209 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 (21.8 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