Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_005454119.1 SACCYDRAFT_RS04825 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >NCBI__GCF_000244975.1:WP_005454119.1 Length = 562 Score = 342 bits (876), Expect = 3e-98 Identities = 218/560 (38%), Positives = 323/560 (57%), Gaps = 25/560 (4%) Query: 12 RSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVK 71 RS+E G + A R+ ++ G+ D +P +G+ ++W+E+TPCN LR LAE K Sbjct: 15 RSREVTDGLERTAA--RAMLRAVGM-GDADFAKPQVGVASSWNEITPCNLSLRRLAEASK 71 Query: 72 RGVYEAGGFPVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGG 126 +GV+ GG+P+EF S + ++ M F R + A VE + +DG VLL G Sbjct: 72 QGVHAGGGYPLEFGTLSVSDGISMGHEGMHFSLVSREVIADSVETVLEAERLDGAVLLAG 131 Query: 127 CDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEM--VKSGEMSLE 184 CDK+ P +LM AA +D+ A+ V G L G+ G+++ T I F + G MS E Sbjct: 132 CDKSLPGMLMAAARLDVAAVFVYAGSTLPGRLDGREL---TIIDAFEAVGACSRGLMSRE 188 Query: 185 EFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRI 244 + E+ + G+C M TA+TMA AEALGM L G+A+ P+VD RR ++ +G + Sbjct: 189 DVDRVERAVCPGEGACGGMYTANTMACAAEALGMALPGSASPPSVDRRRDGFARASGEAV 248 Query: 245 VEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGR 304 V +++ + D+LT+EAFENAI V A+GGSTNAVLHLLA+A V LSLDD+ R+G Sbjct: 249 VGLLRRGITARDVLTREAFENAIAVVMALGGSTNAVLHLLAIAHEAEVALSLDDFSRVGD 308 Query: 305 DVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNY 364 VP + +++P G+++M GG+PVV+KA+ + G LH D +TV+G T+ ++ Sbjct: 309 RVPHLADVKPFGRHVMTAVDRVGGVPVVMKALLDAGHLHGDCLTVTGRTVAENLAEAAPP 368 Query: 365 NEDVILPREKA--LTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYH 422 D + RE + + +GG+ +L G LAP GAV+K +A + +GRA VF+ + Sbjct: 369 ELDGTVIRELSDPIHPTGGVTILHGTLAPEGAVVK--SAGFDRTRFEGRARVFDGEQAAM 426 Query: 423 ARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGI-TDMIRISDARMSG 481 A + ++ ++V++Y GP+G PGM E+ + + + G+ D++ ++D R SG Sbjct: 427 AALP----ELSAGDVVVIRYEGPRGGPGMREM--LAVTGAIKGAGLGRDVLLLTDGRFSG 480 Query: 482 TAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKP 541 G I H APEAA GGP+A V +GD I VD+ +RTL L V D ELARRR W SP Sbjct: 481 GTTGLCIGHVAPEAAHGGPIAFVRDGDPIVVDLSSRTLDLLVEDAELARRRDGW-SPPGI 539 Query: 542 LTGGYGGLYIKTVMQADAGA 561 G G Y + V A GA Sbjct: 540 EHRGVLGKYARLVRSASEGA 559 Lambda K H 0.318 0.135 0.402 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: 905 Number of extensions: 50 Number of successful extensions: 6 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: 579 Length of database: 562 Length adjustment: 36 Effective length of query: 543 Effective length of database: 526 Effective search space: 285618 Effective search space used: 285618 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 (21.7 bits) S2: 53 (25.0 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