Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 319 bits (817), Expect = 2e-91 Identities = 202/511 (39%), Positives = 293/511 (57%), Gaps = 41/511 (8%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 +E RN+TK F V+ L V ++ G ++ L+GENGAGKSTLMK+L+G T GE+ Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTT--GEVV 62 Query: 66 YEGAVR----NFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTF 121 +GAVR RA +E GI++IHQE L L+IA+NIFLG+E+ + + Sbjct: 63 VDGAVRAPGGGSRA---AEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMR 119 Query: 122 NRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181 +TRE L KVGL P+T + + V ++QLVEIA+AL+++ +LLI+DEPTA+L ++E Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179 Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN- 240 L L+ + G+T I I+HKL+EV + D++ V+RDG+ V E + V R Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLV------AREATASVTRRQM 233 Query: 241 ---MVGRDLEDRYPPR-----DVPIGETI--LEVKNWNAYHQQHRDRQVLHDINVTVRKG 290 MVGR+L D +PP+ D T+ L V W ++ VR+G Sbjct: 234 ANLMVGRELADLFPPKLPAPQDGAPAITVRGLTVPGW------------AEGVDFEVRRG 281 Query: 291 EVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDR 350 E++G AGL+GAGRTE + G R G V I G+PV + + R A GL Y++EDR Sbjct: 282 EILGFAGLVGAGRTELFEGLLG--LRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDR 339 Query: 351 KHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLS 410 K GL ++ + N TL L +K +D E + IR+ + +LS Sbjct: 340 KGKGLHVHFGLRPNLTLMALERYAK-PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLS 398 Query: 411 GGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPE 470 GGNQQK+ L+K L P V++LDEPTRG+DVGAK EIY ++ +LA G V++ISSE+ E Sbjct: 399 GGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELME 458 Query: 471 LLGNCDRIYVMNEGRIVAELPKGEASQESIM 501 L+G C R+ VM GR+ L + ++E ++ Sbjct: 459 LIGLCHRVAVMRAGRLQTTLQEPHLTEEELI 489 Lambda K H 0.316 0.135 0.374 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: 588 Number of extensions: 32 Number of successful extensions: 10 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: 512 Length of database: 496 Length adjustment: 34 Effective length of query: 478 Effective length of database: 462 Effective search space: 220836 Effective search space used: 220836 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 (21.6 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