Align ABC transporter related (characterized, see rationale)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 290 bits (742), Expect = 8e-83 Identities = 176/473 (37%), Positives = 273/473 (57%), Gaps = 10/473 (2%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +L + I K Y L + L L GEV AL GENGAGKSTL K++ G + G + F Sbjct: 9 VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 G + A++ GI V QE+NL+P L+VA+NLFL P G I K++ A A Sbjct: 68 QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIA 127 Query: 124 VLTQFKLD-IDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 + Q LD ID + + I QQ++ IAR + VL+LDEPTA L A+EV++LF Sbjct: 128 AMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + +L+A+GVAI++I+H L+++ +++ RI VLR+G + A +L+ M+GR L Sbjct: 188 ITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELG 247 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 E + + A L+++ +S ++ ++ V G+ G++GL+G+GR+E+ Sbjct: 248 EHI------DLGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLR 301 Query: 303 AVFGLDLVDSGSIHLAG--QKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA 360 +FG D DSG++ L Q +++ P DA+ GIAL EDRK +G++ SI NI L Sbjct: 302 LIFGADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALG 361 Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420 I +++ + +AQ ID ++I + + + +LSGGNQQKV++ RWL E Sbjct: 362 NMPVISSGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECS 421 Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 +L+ DEPTRGID+GA +I L+ L +G +L+V SS+L EL+ +++ VL Sbjct: 422 VLLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVL 474 Score = 77.8 bits (190), Expect = 9e-19 Identities = 62/225 (27%), Positives = 110/225 (48%), Gaps = 10/225 (4%) Query: 20 LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQH---FNTPMDA 76 + DVS + +GE+ + G GAG++ L++++ GA + D G + LG P +P DA Sbjct: 273 VRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADAADSGTVA-LGSPAQVVSIRSPADA 331 Query: 77 QKAGISTVYQE---VNLVPNLTVAQNLFLGYEP--RRLGLIHFKKMYADARAVLTQFKLD 131 GI+ + ++ L+ +++ N+ LG P G+++ A A+ + ++ Sbjct: 332 VGHGIALITEDRKGEGLLLTQSISANIALGNMPVISSGGIVNSGDEMALAQRQIDAMRIR 391 Query: 132 IDVSAPL-SDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190 A L S+ S QQ + I R + VL+ DEPT +D ++ +L +L +G Sbjct: 392 SSSPAQLVSELSGGNQQKVVIGRWLERECSVLLFDEPTRGIDVGAKFDIYALLGELTRQG 451 Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEA 235 A+V ++ L ++ I DRI VL G+ I + Q L+ A Sbjct: 452 KALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAA 496 Score = 69.7 bits (169), Expect = 2e-16 Identities = 52/202 (25%), Positives = 96/202 (47%), Gaps = 5/202 (2%) Query: 274 IQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISA 333 + ++LT+ +G+ + L G G+G+S + + GL +G + G+ A Sbjct: 24 LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEEL 83 Query: 334 GIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPD 393 GI + ++ + + LS+ EN+ L G W R+ IA + ++ + D Sbjct: 84 GIRMVMQELNL---LPTLSVAENLFLDNLPSNGGWISRKQLRKAAIAA--MAQVGLDAID 138 Query: 394 ADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSL 453 D + +L G+QQ V +AR L + +L+LDEPT + + + I L G+++ Sbjct: 139 PDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAI 198 Query: 454 LVASSELDELVAFSNKVVVLRD 475 + S L+EL + ++ VLRD Sbjct: 199 IYISHRLEELARVAQRIAVLRD 220 Lambda K H 0.319 0.136 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: 564 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 499 Length of database: 517 Length adjustment: 34 Effective length of query: 465 Effective length of database: 483 Effective search space: 224595 Effective search space used: 224595 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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