Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate GFF2269 PS417_11570 ABC transporter permease
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__WCS417:GFF2269 Length = 281 Score = 150 bits (380), Expect = 2e-41 Identities = 84/259 (32%), Positives = 153/259 (59%), Gaps = 8/259 (3%) Query: 9 LVLF---VFLPNLMIIGTSFLTRDDASFVKM-VFTLDNYTRLLDPLYF-EVLLHSLNMAL 63 LVLF + LP + + SF D VK +T +Y LL YF E+ + ++ Sbjct: 12 LVLFAGLLILPLGLTLVLSFNVFDYQVGVKADEWTFAHYLSLLSDSYFYEIFWRTFWISA 71 Query: 64 IATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYLNEF 123 + TL C+++G P A+ L+++ R + L L++ P + ++R +G + L G +N+ Sbjct: 72 LVTLLCVLIGVPEAYILSRMGTPWRSIFLILILTPLLISVVVRAFGWSLLLGADGLVNQV 131 Query: 124 LLWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGASKLQ 183 + +LG P+++++TP AVII LV+++LPFM++P+++S++KLD +AA LGAS+ Sbjct: 132 IQFLG--GRPVKLLYTPFAVIIALVHVMLPFMIIPVWTSLQKLDPSAEQAALSLGASQAT 189 Query: 184 TFIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDWPFG 243 +I++P MPG+++G L+V A F + L+GG + ++ V+ Q+L+ +WP G Sbjct: 190 VMRKIVLPQVMPGVLSGTLIVFGLAASSFAIPGLLGGRRLKMVATVVYDQYLSELNWPMG 249 Query: 244 AATSITLTIVMGLMLLVYW 262 A ++ L +V L++++ W Sbjct: 250 ATIAVVLLLV-NLLIMLSW 267 Lambda K H 0.333 0.148 0.456 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: 281 Number of extensions: 18 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: 275 Length of database: 281 Length adjustment: 25 Effective length of query: 250 Effective length of database: 256 Effective search space: 64000 Effective search space used: 64000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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