Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_061946568.1 CPter91_RS23415 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_001584185.1:WP_061946568.1 Length = 333 Score = 194 bits (492), Expect = 4e-54 Identities = 114/335 (34%), Positives = 179/335 (53%), Gaps = 12/335 (3%) Query: 13 TTMANTASAQGLRARLFNPAA---RQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQS 69 TT + ++S R FN + + L +LL M FS S NF+ ++ Sbjct: 2 TTSSRSSSRLSSRWSSFNGSISGLKNYLGLIGALLAMCALFSVLSENFLTAATFTTLSND 61 Query: 70 TAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALS 129 V+A+ T+V+I GIDLSVG++M A + + + WG PL A+ +L Sbjct: 62 IPTLVVMAVGMTFVLIIGGIDLSVGSVMALAASVLSMAMVRWGWPLFTAGILAMLVASLC 121 Query: 130 GWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLI 189 G ++G++ ++P FI +LG++ + +GL+ ++ +R Y I+ L G Sbjct: 122 GMVTGLISVGWRIPSFIVSLGVLEMARGLAYQVTNSRTEYIGSA--VDGISSPILFG--- 176 Query: 190 PSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFS 249 + A + ++ I ++L KTV GR+ +G+NEEA+RL+G+ KV V+ Sbjct: 177 ----MSPAFISAIVIVIVGHLVLTKTVLGRHWIGIGTNEEAVRLAGINPRPPKVLVFALM 232 Query: 250 GAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSV 309 G + G+ L SRL +A P G G EL IAAVVIGGTSL GG G+++ T IG I+SV Sbjct: 233 GLLAGVGALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSVISTFIGVLIISV 292 Query: 310 LVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344 L GL + V++ + ++TG++I+ AV LD RRR Sbjct: 293 LEAGLAQVGVSEPMKRIITGLVIVAAVVLDTYRRR 327 Lambda K H 0.326 0.139 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: 247 Number of extensions: 14 Number of successful extensions: 3 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: 347 Length of database: 333 Length adjustment: 28 Effective length of query: 319 Effective length of database: 305 Effective search space: 97295 Effective search space used: 97295 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 24 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