Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_047006477.1 AAW01_RS01960 ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_001010925.1:WP_047006477.1 Length = 315 Score = 99.8 bits (247), Expect = 1e-25 Identities = 73/221 (33%), Positives = 117/221 (52%), Gaps = 12/221 (5%) Query: 1 MANTILEMRNITKTFPG-VKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSG-VYPAG 58 M + IL++R++ KT+ G VKAL V+L ++ GEI AL+G NGAGK+TL+ + G V P G Sbjct: 1 MTDPILDIRDLEKTYDGGVKALGGVDLTIRAGEIFALLGPNGAGKTTLIGAVCGMVRPTG 60 Query: 59 TYEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQ 118 G I G +DIG++ QEL+ ++ + S G+ Sbjct: 61 ---GTIRAFGMDMATHWKAARKDIGLV--PQELSFDMFDTVIRQVRF-----SRGMFGCP 110 Query: 119 QTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178 ++LK + L + ++ I ++ G ++ V IAKALS KLL LDEPTA ++ Sbjct: 111 PDEAVIEDILKSLSLWDKRDSQIRELSGGMKRRVMIAKALSHDPKLLFLDEPTAGVDVEL 170 Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDG 219 + + R +G+T I+ TH + E ++AD++ V+ G Sbjct: 171 RRDMWRQIDALRTRGVTIILTTHYIEEAEEMADRVGVISKG 211 Score = 67.4 bits (163), Expect = 7e-16 Identities = 56/213 (26%), Positives = 107/213 (50%), Gaps = 21/213 (9%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L +++T+R GE+ + G GAG+T +V G R TG I +D++T K Sbjct: 20 KALGGVDLTIRAGEIFALLGPNGAGKTTLIGAVCGMV---RPTGGT-IRAFGMDMATHWK 75 Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLAN-LAGV--SKASIIDDIKEMKVASDFRTR 394 A + V ++ L + D ++ + + G +A I D +K + + ++ Sbjct: 76 AARKDIGLVPQE---LSFDMFDTVIRQVRFSRGMFGCPPDEAVIEDILKSLSLWDKRDSQ 132 Query: 395 LRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQL 454 +R LSGG +++V+++K L +P +L LDEPT G+DV + +++ I+ L Sbjct: 133 IR-----------ELSGGMKRRVMIAKALSHDPKLLFLDEPTAGVDVELRRDMWRQIDAL 181 Query: 455 AADGKGVLMISSEMPELLGNCDRIYVMNEGRIV 487 G +++ + + E DR+ V+++GRI+ Sbjct: 182 RTRGVTIILTTHYIEEAEEMADRVGVISKGRIL 214 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: 359 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 315 Length adjustment: 31 Effective length of query: 481 Effective length of database: 284 Effective search space: 136604 Effective search space used: 136604 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: 50 (23.9 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