Align putrescine transport system permease protein PotH (characterized)
to candidate Pf6N2E2_1745 Spermidine Putrescine ABC transporter permease component PotB (TC 3.A.1.11.1)
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1745 Length = 393 Score = 147 bits (370), Expect = 5e-40 Identities = 84/241 (34%), Positives = 139/241 (57%), Gaps = 5/241 (2%) Query: 61 RAIPPYTELMEWADGQLSITLNLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPL 120 RA P YT + L T + G D +Y D ++L++A + + CLL+G+P Sbjct: 137 RASPAYTSYYLLSALDLERTAH-GIQRVAPDKRVYLDLTFKTLKIAFVVSVLCLLLGFPF 195 Query: 121 AWAVAHSKPSTRNILLLLVILPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTI 180 A + + + +L+L V+LP WTS L R AW+ +L+ G++N LL LG+I+QPL + Sbjct: 196 AVLLVKASRPFQMLLILAVMLPFWTSLLARTTAWIVVLQEKGIVNTLLLKLGLIEQPLPM 255 Query: 181 LHTNLAVYIGIVYAYVPFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGG 240 + L VYI +V+ +PF VLP+Y+ + I + A+ LGA P++ F V +P+T G Sbjct: 256 IFDALGVYIVMVHILLPFTVLPLYSVMKGIPAHYMRASQSLGAHPVRGFLHVYLPMTLTG 315 Query: 241 IIAGSMLVFIPAVGEFVIPELLGGPDSIMIGRVLWQEFFNNR--DWPVASAVAIIMLLLL 298 I +G++L FI A G +V P L+G M+G + F+ N +W +ASA+ ++++L + Sbjct: 316 IGSGTLLTFIVAAGYYVTPTLVGSAREQMLGYFI--AFYTNTTVNWGMASALGLVLILCV 373 Query: 299 I 299 + Sbjct: 374 M 374 Lambda K H 0.328 0.144 0.457 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: 292 Number of extensions: 16 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: 317 Length of database: 393 Length adjustment: 29 Effective length of query: 288 Effective length of database: 364 Effective search space: 104832 Effective search space used: 104832 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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