Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 292 bits (748), Expect = 2e-83 Identities = 172/511 (33%), Positives = 282/511 (55%), Gaps = 11/511 (2%) Query: 1 MNGQMSELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSIL 60 M+ + ++ PV++ + K+F L DV + + PGE HAL+G+NGAGKSTL+ +L Sbjct: 5 MDASTAHAPAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVL 64 Query: 61 TGLRKPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQP---- 116 TG+ + G++R G A + A R ++ VYQ + +LSVAEN+F R P Sbjct: 65 TGVLEASGGQMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGI 124 Query: 117 LRGGVIDWQAMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDE 176 +G IDW + + AR L+ + + D V +QLV IARALS +R +ILDE Sbjct: 125 AQGFRIDWATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDE 184 Query: 177 PTAQLDGDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSA 236 PT+ LD DE+++LF + L+ EG++ +F++H L +VY + +TVLR+ + Sbjct: 185 PTSSLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKD 244 Query: 237 LPREQLIEAMTGERGGLAVADAAARGALPADTAVALELKELTGAD--YEGVSFTVKRGEV 294 L + LI AM G A A A+ + A L+ + L G D + + ++ GEV Sbjct: 245 LGPQALIAAMLGRDLAAASEQPAPAPAVDSRHANLLQAEGL-GQDTQLQPLDLQIRAGEV 303 Query: 295 VGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEG 354 VGL G SGRT +A + GL RG + +DG ++ + ++ HG+ P++R +G Sbjct: 304 VGLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDG 363 Query: 355 LVLTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQ 414 +V SV EN ++ + +G + +++ ++ + LGI + + + LSGGNQ Sbjct: 364 IVAELSVRENIALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQ 423 Query: 415 QKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRT 473 QK ++AR +A P +L+L +PT G+DV +K+ ++ + R+ + G AVL +S E+ + +R Sbjct: 424 QKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRV 483 Query: 474 CDRVLVMFRGRVAAEFPAGWQD---HDLIAS 501 R++V+ R E PAG + +DLIA+ Sbjct: 484 AHRIVVLRDRRKVGELPAGSSEDAVYDLIAA 514 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: 587 Number of extensions: 26 Number of successful extensions: 6 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: 510 Length of database: 517 Length adjustment: 35 Effective length of query: 475 Effective length of database: 482 Effective search space: 228950 Effective search space used: 228950 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 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