Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate WP_005456798.1 SACCYDRAFT_RS13145 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >NCBI__GCF_000244975.1:WP_005456798.1 Length = 560 Score = 323 bits (827), Expect = 1e-92 Identities = 218/538 (40%), Positives = 298/538 (55%), Gaps = 21/538 (3%) Query: 25 RSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAGGFPVEFPVF 84 R+ ++ G D +F RP IG+ ++LTPCN +LA G+ +AGG + F Sbjct: 20 RAMLRAVGFADEDFT-RPQIGVAAAANDLTPCNIALDRLAGATADGVRKAGGVAMRFSTI 78 Query: 85 SN------GESNLRPSAMLTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAASC 138 + G +R S + +R+L + VE + +DA+V +AGCDK+ P +LM AA Sbjct: 79 AMSDGIAMGHRGMRAS-LPSRDLIADSVECVMEAEQLDAMVTIAGCDKSLPGMLMAAARL 137 Query: 139 DVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGEIDVHHFLSAEAGMSRSAGTCN 198 +VP + GG L G +G+ + + V++ A +G + E AG+C Sbjct: 138 NVPTAFLYGGSSLPGSWQGRPV-TIQDVFEAVGAQASGLLSTDDLDELERAACPGAGSCA 196 Query: 199 TMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEMALEGLVLSKILTRA 258 M TA+T+A AEALG+ALP +A+ PA+D R +AH +G V G+ ILTR Sbjct: 197 GMYTANTIAAEAEALGIALPGSASAPAIDPTRPGIAHDTGAAAVAALRAGIRPRDILTRE 256 Query: 259 AFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTIVDLMPSGRFPME 318 AFENAI A+GGSTNA +HL AIA GV L L+D+ RI R TP I DL P GR M Sbjct: 257 AFENAITVVMALGGSTNAALHLPAIAHEAGVRLTLDDFDRISRHTPHIADLRPGGRHVMA 316 Query: 319 EFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVRE--APNYDEEVIRPLDRPLIA 376 + + GG+PAVL L + GLL + D LTV G +L +N+ E AP D V+R D PL Sbjct: 317 DLHQVGGVPAVLAALLDAGLL-HGDCLTVTGATLAENLAELAAPKPDGTVLRTPDDPLRP 375 Query: 377 DGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSVM 436 DGG+ ILRG LAP GAV+K + + + + G A VF+N D ++ L A V+ Sbjct: 376 DGGLAILRGALAPSGAVVKMAGLTVD--RFHGTARVFDNEDAAMGYVSGGRL--TAGEVI 431 Query: 437 VLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVR-ISDARMSGTAYGTVVLHVAPEAAA 495 V++ GPRG PGM E+ + + + G+ D V ++D R SG G V HVAPEAAA Sbjct: 432 VIRYEGPRGGPGMPEM--LAVTAAVRGTGLGDQVALVTDGRFSGATTGLCVGHVAPEAAA 489 Query: 496 GGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAPGVAGQLGKGGYARL 553 GGPLA V +GD I +D A T+ LD+ EL RR P AP G L K Y+RL Sbjct: 490 GGPLALVADGDPIMIDIPARTIDLDVNPAELERRRHRWHPPPAPTGNGFLAK--YSRL 545 Lambda K H 0.319 0.136 0.412 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: 870 Number of extensions: 44 Number of successful extensions: 7 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: 583 Length of database: 560 Length adjustment: 36 Effective length of query: 547 Effective length of database: 524 Effective search space: 286628 Effective search space used: 286628 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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