Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >NCBI__GCF_000469325.1:WP_022530418.1 Length = 508 Score = 275 bits (702), Expect = 4e-78 Identities = 165/472 (34%), Positives = 255/472 (54%), Gaps = 10/472 (2%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73 V+ + K F AL+DV + + GE HAL+G NGAGKSTL+ ++TG+ + +G V Sbjct: 13 VLSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTL 72 Query: 74 SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133 G ++A ++ VYQ + +LSVAEN++I RQP+R G IDW M DA Sbjct: 73 HGQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQIDWHRMNADAVK 132 Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193 LL+ I V SV +Q++ IARA+ A +ILDEPT+ LD +E+ +LF I Sbjct: 133 LLESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFAII 192 Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253 L+ + + LF++H + +VY I +TVLR+ R+I LP L+ M G++ Sbjct: 193 RHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIGQK--- 249 Query: 254 AVADAAARGALPADTAVALELKELTGADYEGV----SFTVKRGEVVGLTGATSSGRTSVA 309 DA + P+ + + G+ S V+ GEV+GL G SGRT VA Sbjct: 250 -FVDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVA 308 Query: 310 EAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTI 369 E + G+ G I V + + +LA +G +DR G+V S+ EN +++ Sbjct: 309 ELLFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSL 368 Query: 370 ARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNV 429 G I K+ QK ID L I E + LSGGNQQKV++AR LAT+P + Sbjct: 369 QAKKGLRRIPL-KKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKL 427 Query: 430 LVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVM 480 L+L +PT G+D+ +K + +++ ++ +G A++ +S E +++ RTCDR++V+ Sbjct: 428 LILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVL 479 Score = 83.6 bits (205), Expect = 2e-20 Identities = 63/244 (25%), Positives = 119/244 (48%), Gaps = 9/244 (3%) Query: 10 SSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG 69 S+V V +++KR ++D S+ V GE L G G+G++ + +L G+ D G Sbjct: 265 STVRFVRMEDISKR----GLVHDFSMAVRAGEVLGLAGLLGSGRTEVAELLFGVTHFDDG 320 Query: 70 EVRFSGAAAPSIADRDAWRERVACVYQH---STIIRDLSVAENLFINRQPLRG-GVIDWQ 125 + + R A +++ + S I+ DLS+ EN+ ++ Q +G I + Sbjct: 321 VIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQAKKGLRRIPLK 380 Query: 126 AMRRDARALLDHWKIDVRE-DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGD 184 + A+ +D I + + GDLS +Q V +AR L+ + +ILDEPT +D + Sbjct: 381 KQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKLLILDEPTRGIDIN 440 Query: 185 EIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIE 244 + + I +L R+G+ +FIS +E+ C + VLRD + + + ++ +++ Sbjct: 441 TKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGELTDNQISQDNIMK 500 Query: 245 AMTG 248 + G Sbjct: 501 VIAG 504 Lambda K H 0.318 0.134 0.377 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: 535 Number of extensions: 28 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 508 Length adjustment: 34 Effective length of query: 476 Effective length of database: 474 Effective search space: 225624 Effective search space used: 225624 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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