Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 306 bits (785), Expect = 8e-88 Identities = 181/465 (38%), Positives = 270/465 (58%), Gaps = 7/465 (1%) Query: 15 LSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAIS 74 ++K F V+ L V F+L+ G + LLGENGAGKSTL+K L G G + ++G + Sbjct: 10 VTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGAVRA 69 Query: 75 PKNTAHAQQL-GIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASY 133 P + A + GI ++QE NL ++++A N+F+G E KR L K M ++ E +A Sbjct: 70 PGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTREALAKV 129 Query: 134 GFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRD 193 G LD + + VA +Q+V I RA+ +A++LI+DEPTA+L E E LF LM L+ Sbjct: 130 GLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALMAGLKA 189 Query: 194 RGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDTHALQR 253 GV++I+++H LD+V + +D + V+R+G V T + + ++ +M+GREL Sbjct: 190 AGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGREL-ADLFPP 248 Query: 254 AGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPAD 313 P + G D EVR GEI+G AGL+G+GRTE E + G++P Sbjct: 249 KLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRT 308 Query: 314 SGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENI-ILALQA-QRGWLR 371 +GT I G+P L+SP A+ G+ + EDRK G+ +R N+ ++AL+ + WL Sbjct: 309 AGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALERYAKPWLD 368 Query: 372 PISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTR 431 P + +Q +++ GIRT S E LSGGNQQK+ L++ L P ++LDEPTR Sbjct: 369 PAA---EQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTR 425 Query: 432 GIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMR 476 G+DVGA EI L++ L GLA++VISSEL EL+G RV +MR Sbjct: 426 GVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMR 470 Score = 74.3 bits (181), Expect = 9e-18 Identities = 58/230 (25%), Positives = 112/230 (48%), Gaps = 19/230 (8%) Query: 26 DNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLG 85 + VDF +RRGEI+ G GAG++ L + L G+ GT+ + GQ + K+ A + G Sbjct: 272 EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHG 331 Query: 86 IGTVYQE---------VNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASYGF- 135 + + ++ L PN+++ + + R K + L + E + +G Sbjct: 332 LTYLSEDRKGKGLHVHFGLRPNLTL---MALERYAKPW--LDPAAEQAALREAVQEFGIR 386 Query: 136 --SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRD 193 SL+VR + S QQ +A+ + + V++LDEPT +D ++ L+++L + Sbjct: 387 TGSLEVRA--SSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAE 444 Query: 194 RGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243 +G+++I ++ L ++ + R+ V+R G + L + EL+ G Sbjct: 445 QGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATG 494 Score = 65.5 bits (158), Expect = 4e-15 Identities = 55/228 (24%), Positives = 105/228 (46%), Gaps = 15/228 (6%) Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 K +G + ++PG + GL G G+G++ +++ G + +G ++ G +R Sbjct: 12 KEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGA---VR 68 Query: 328 SP----HQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAE 383 +P A GI ++ + ++ +NI L + +RG + K +E Sbjct: 69 APGGGSRAAEAQGIVLIHQEFN---LADDLTIAQNIFLGHEIKRGLF--LDDKAMREKTR 123 Query: 384 RFIRQLGIRT-PSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEII 442 + ++G+ P T + L +Q V ++R L + LI+DEPT + G + Sbjct: 124 EALAKVGLPLDPDTR--VRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLF 181 Query: 443 RLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELS 490 L+ L A G+ ++ IS +L+E+ D V++MRD VA A ++ Sbjct: 182 ALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVT 229 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: 580 Number of extensions: 37 Number of successful extensions: 8 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: 496 Length adjustment: 34 Effective length of query: 466 Effective length of database: 462 Effective search space: 215292 Effective search space used: 215292 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 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