Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Pf6N2E2_3128 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3128 Length = 345 Score = 169 bits (427), Expect = 1e-46 Identities = 96/233 (41%), Positives = 139/233 (59%), Gaps = 6/233 (2%) Query: 37 QVLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDI 96 QV + G V V+ + + I GE F ++G SGSGK+T +R P++G+I + GE+ Sbjct: 9 QVSRQFGDVKAVDRVCIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIHGEEA 68 Query: 97 LQLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTV 156 L ++R ++ VFQ + L PH +V DNVAYGLKV+G +K +RA + V Sbjct: 69 T-----GLAPYQRD-VNTVFQDYALFPHMNVRDNVAYGLKVKGVAKAERIKRADEALEMV 122 Query: 157 GLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQK 216 L GY + P QLSGG RQRV LARAL ++L+DE ALD +R +MQ +L +LQ+ Sbjct: 123 ALGGYGERKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQR 182 Query: 217 TLHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 L T +F+THD EA+ + +R+A+ G++ QV TPR + PA +V FV Sbjct: 183 QLGITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATTFVAEFV 235 Lambda K H 0.321 0.138 0.387 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: 216 Number of extensions: 8 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: 276 Length of database: 345 Length adjustment: 27 Effective length of query: 249 Effective length of database: 318 Effective search space: 79182 Effective search space used: 79182 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 (21.9 bits) S2: 48 (23.1 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