Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 233 bits (594), Expect = 1e-65 Identities = 163/506 (32%), Positives = 269/506 (53%), Gaps = 25/506 (4%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L ++NITK F + A NVNL + GEI AL+GENGAGK+TLM +L G Y A EG + Sbjct: 10 LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVAD--EGRV 67 Query: 65 HYE---GAVRNFR--AINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQ 119 G + + A + + GI ++HQ L L+ ENI LG E S + Sbjct: 68 MVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSK 127 Query: 120 TFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDS 179 + +EL++ GL+ + ++ + VG++Q VEI KAL + ++L+LDEPTA L +S Sbjct: 128 ARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQES 187 Query: 180 EALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTV---KTLDCHQEEISEDV 236 ++L N L +GM I I+HK+ EV +D++ VLR G V T C + +++E + Sbjct: 188 DSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELM 247 Query: 237 IIRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIA 296 + + + E P GE IL K +A R+++ ++N+++RKGE++G+A Sbjct: 248 VGHAVQMAEREPGNP------GEEILVFKGVSA----GEGRELIENVNLSLRKGEIIGLA 297 Query: 297 GLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLV 356 G+ G G++ A + G G V + +P+ + AI +G+A + EDR H G+V Sbjct: 298 GVSGNGQSMLAKVLSGLE--EPTAGAVTLGSQPLKANAA-AAIQSGVARIPEDRHHDGIV 354 Query: 357 LNDNILHNTTLANL--AGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQ 414 ++ N L + + ++ + K A + IR SG + LSGGN Sbjct: 355 GAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNI 414 Query: 415 QKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGN 474 QK+VL++ L P +++ +P+RG+DVGA +++ + + G GVL+IS ++ EL Sbjct: 415 QKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQL 474 Query: 475 CDRIYVMNEGRIVAELPKGEASQESI 500 DRI V++ G + + E ++ + Sbjct: 475 SDRIAVIHRGHVSEPMASEELDKKQV 500 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: 600 Number of extensions: 46 Number of successful extensions: 8 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: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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 24 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