Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 306 bits (784), Expect = 1e-87 Identities = 182/470 (38%), Positives = 268/470 (57%), Gaps = 7/470 (1%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L G+ K + L +D +L RGE++AL GENGAGKSTL K + G+ G + Sbjct: 9 VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 +G+ P + A++LGI V QE+NLLP +SVA+NLF+ P G + RK++ K A Sbjct: 68 QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIA 127 Query: 129 LMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 MA G ++D + + QQ+V I R + VLILDEPTA L +EVE+LF+ Sbjct: 128 AMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 + +L+ RGV++I+++H L+++ +V+ RI VLR+G+ V +LV +M+GREL Sbjct: 188 ITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELG 247 Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 H + R + P K + + EVR GEI G++GL+G+GRTE +IF Sbjct: 248 EH-IDLGPRHI--GAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIF 304 Query: 308 GIKPADSGTALIKGKPQ--NLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365 G ADSGT + Q ++RSP A GI EDRK +G++ S+ NI L Sbjct: 305 GADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMP 364 Query: 366 QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLI 425 ++ ++ +A+R I + IR+ S Q + LSGGNQQKV++ RWL L+ Sbjct: 365 VISSGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLL 424 Query: 426 LDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475 DEPTRGIDVGA +I L+ L G AL+V+SS+L EL+ DR+ ++ Sbjct: 425 FDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVL 474 Score = 89.0 bits (219), Expect = 4e-22 Identities = 66/218 (30%), Positives = 109/218 (50%), Gaps = 7/218 (3%) Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339 DL + GE++ L G G+G++ +++I G+ +G +G+ S QA LGI Sbjct: 28 DLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEELGIRM 87 Query: 340 CPEDRKTDGIIAAASVRENIILA-LQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQ 398 ++ ++ SV EN+ L L + GW ISRK+ ++ A + Q+G+ + Sbjct: 88 VMQELN---LLPTLSVAENLFLDNLPSNGGW---ISRKQLRKAAIAAMAQVGLDAIDPDT 141 Query: 399 PIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVI 458 + L G+QQ V ++R L+ LILDEPT + + I L A G+A++ I Sbjct: 142 LVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYI 201 Query: 459 SSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMN 496 S LEEL A R+ ++RD V P+A + ++N Sbjct: 202 SHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVN 239 Score = 74.3 bits (181), Expect = 9e-18 Identities = 62/220 (28%), Positives = 106/220 (48%), Gaps = 8/220 (3%) Query: 27 NVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL--EGQAISPKNTAHAQQL 84 +V F +R GEI + G GAG++ L++ + G AD GT+ L Q +S ++ A A Sbjct: 275 DVSFEVRSGEIFGISGLIGAGRTELLRLIFGADAADSGTVALGSPAQVVSIRSPADAVGH 334 Query: 85 GIGTVYQE---VNLLPNMSVADNLFIGREP--KRFGLLRR-KEMEKRATELMASYGFSLD 138 GI + ++ LL S++ N+ +G P G++ EM ++ A S Sbjct: 335 GIALITEDRKGEGLLLTQSISANIALGNMPVISSGGIVNSGDEMALAQRQIDAMRIRSSS 394 Query: 139 VREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSL 198 + ++ S QQ V I R ++ VL+ DEPT +D ++ L+ +L +G +L Sbjct: 395 PAQLVSELSGGNQQKVVIGRWLERECSVLLFDEPTRGIDVGAKFDIYALLGELTRQGKAL 454 Query: 199 IFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELV 238 + V+ L ++ + DRI VL G + E Q +L+ Sbjct: 455 VVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLL 494 Lambda K H 0.321 0.138 0.391 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: 570 Number of extensions: 24 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: 3 Length of query: 500 Length of database: 517 Length adjustment: 34 Effective length of query: 466 Effective length of database: 483 Effective search space: 225078 Effective search space used: 225078 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