Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Phaeo:GFF2651 Length = 522 Score = 225 bits (573), Expect = 3e-63 Identities = 157/497 (31%), Positives = 257/497 (51%), Gaps = 10/497 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L ++NITK F V A ++V+ + GE+ AL+GENGAGK+TLM +L G Y A T G + Sbjct: 15 VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADT--GGV 72 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 GA A + D G+ ++HQ L L++ ENI LG E + R Sbjct: 73 ELFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARI 132 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 R L ++ LK P ++ + VG++Q VEI KAL + ++LILDEPTA L +S+AL Sbjct: 133 RALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFA 192 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 L E N+G++ I I+HKL+EV ++D++ VLR G V + + D + MVG Sbjct: 193 TLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLV--AERQTADTDSDALAALMVGA 250 Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304 D+ + P G +L++++ L +++ + G++ G+AG+ G G+ Sbjct: 251 DVVPAKFAANTP-GPALLQLRDVTT--PSAGASPGLRHVSLDLAAGQITGLAGVSGNGQA 307 Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364 + V G +G + ++G + R+AI AG+A + EDR G + + ++ N Sbjct: 308 ALSDLVSGLITPQ--SGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTEN 365 Query: 365 TTLANLA-GVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 L A S +D A T +R G LSGGN QK++L + L Sbjct: 366 AILETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVL 425 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 +P +++ ++P RG+D+GA ++ + + A G VL+IS ++ E++ D I+V++E Sbjct: 426 EQSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISE 485 Query: 484 GRIVAELPKGEASQESI 500 GR+ +G E + Sbjct: 486 GRLSPGFARGSKQPEEL 502 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: 543 Number of extensions: 29 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: 522 Length adjustment: 35 Effective length of query: 477 Effective length of database: 487 Effective search space: 232299 Effective search space used: 232299 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