Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_084938181.1 HA51_RS25215 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_002095475.1:WP_084938181.1 Length = 355 Score = 224 bits (572), Expect = 2e-63 Identities = 133/327 (40%), Positives = 192/327 (58%), Gaps = 28/327 (8%) Query: 36 KLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGT 95 K F +LL+++ FFSF PNF+ NL+ + Q A+ G+LAI T VI+T GIDLSVG Sbjct: 13 KARTFIALLIVVGFFSFMVPNFLTTSNLLIMTQHVAITGLLAIGMTLVILTGGIDLSVGA 72 Query: 96 MMTFCAVMAGVVLTNWGMPL----------PLGIAAAIFFGALSGWISGMVIAKLKVPPF 145 + C ++AG +LTN G+PL P I FG + G+I+G V+ +L V PF Sbjct: 73 VAGICGMVAGALLTN-GVPLWGGNTLFFNVPEVILVVALFGIVLGFINGAVVTRLGVAPF 131 Query: 146 IATLGMMMLLKGLSLVISGTRPIYFN-------DTEGFSAIAQDSLIGDLIPS-LPIPNA 197 I TLGMM + +G +L+ + Y N GF+ + SL+G IP L + Sbjct: 132 ICTLGMMYVARGAALLFNDGST-YANLVGMPALGNTGFAFLGSGSLLGVYIPIWLMVGFL 190 Query: 198 VLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAG 257 +L L+L KT GRY +A G NE A RL+GV + KV VY FSG + G Sbjct: 191 LLGLYLT--------RKTPLGRYIYATGGNESAARLAGVPIIKVKVFVYAFSGLCAALVG 242 Query: 258 LIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIM 317 LI+AS+L +A P G +E+DAI A V+GGT+L+GG G + G+IIGAF++ L +G+ +M Sbjct: 243 LIVASQLQTAHPMTGNMFEMDAIGATVLGGTALAGGRGRVSGSIIGAFVIVFLADGMVMM 302 Query: 318 SVAQEWQTVVTGVIIILAVYLDILRRR 344 V+ WQ V+ G++I+ AV +D +++ Sbjct: 303 GVSDFWQMVIKGLVIVTAVVIDQFQQK 329 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: 262 Number of extensions: 15 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: 355 Length adjustment: 29 Effective length of query: 318 Effective length of database: 326 Effective search space: 103668 Effective search space used: 103668 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