Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate RR42_RS31070 RR42_RS31070 dihydroxy-acid dehydratase
Query= reanno::WCS417:GFF2156 (578 letters) >FitnessBrowser__Cup4G11:RR42_RS31070 Length = 576 Score = 505 bits (1300), Expect = e-147 Identities = 284/557 (50%), Positives = 354/557 (63%), Gaps = 5/557 (0%) Query: 22 FMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEF 81 F+ ++++K G D +P+IGI NT S PC+ + Q+ E VKRGV+ AGG PV+F Sbjct: 24 FLRKAFIKGAGYTDDAL-SRPVIGIVNTNSSYNPCHGNAPQLVEAVKRGVMLAGGLPVDF 82 Query: 82 PVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASCDVP 141 P S ES PT+M RNL SMD EE IR P+D VVL+ GCDKT PA LMGAAS VP Sbjct: 83 PTISVHESFSAPTSMYLRNLMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQLMGAASAGVP 142 Query: 142 AIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFLAAEGGMSRSAGTCNTMG 201 AI + G ML G H+G+ +G+ T + + +A I + + S GTC+ MG Sbjct: 143 AIQLVTGSMLTGSHRGERVGACTDCRRYWGRYRAEEIDAPEIADVNNQLVASVGTCSVMG 202 Query: 202 TASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTKEAFE 261 TASTMAC+ EALG + A+ PAV A R +A +G AV M R L +ILT A E Sbjct: 203 TASTMACLTEALGMMVAGGASAPAVTADRVRVAERTGTTAVAMARSGLTPERILTGRAIE 262 Query: 262 NAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMPTIVDLQPSGRFLMEEFY 321 NAIRV AIGGSTN ++HL AIAGR+G+ +DL R+ R P +VDL+PSG+ ME+F+ Sbjct: 263 NAIRVLLAIGGSTNGIVHLTAIAGRLGIGIDLAGLDRMSRETPVLVDLKPSGQHYMEDFH 322 Query: 322 YAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDSPIYGQDEVIRTLDNPIRADGGI 381 AGG+PA+LR E + H + LTV+G++LGE +P EVIR D PI GG+ Sbjct: 323 AAGGMPALLR---ELRPLLHLDTLTVSGRTLGEELDAAPAPFAQEVIRPFDAPIYPVGGL 379 Query: 382 CVLRGNLAPLGAVLKPSAASPALMQHRGRAVVFENFDMYKARINDPELDVDANSILVMKN 441 VLRGNLAP GA++K SAA P LM+H GRAVVFE+ + RI+D LDV A+ ILV+K Sbjct: 380 AVLRGNLAPGGAIIKQSAADPVLMEHEGRAVVFEDAEDMALRIDDDALDVKADDILVLKR 439 Query: 442 CGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLA 501 GP G PGM E G M +P KL GV DMVRISD RMSGTA GT+VLHV PEAA GGPLA Sbjct: 440 IGPTGAPGMPEAGYMPIPRKLARAGVKDMVRISDGRMSGTAAGTIVLHVTPEAAIGGPLA 499 Query: 502 TVKEGDWIELDCANGRLHLDIPDAELAARMADLAPPQKLIVGGYRQLYIDHVLQADQGCD 561 V+ GD I L A + L I DAELA R A+ + GYR+L++ V QADQG D Sbjct: 500 HVRNGDRIRLSVARREISLLIDDAELARRAAEHEVVRPAAERGYRKLFLATVTQADQGVD 559 Query: 562 FDFLVGCRGAE-VPRHS 577 FDFL R +E VPR S Sbjct: 560 FDFLRAARTSETVPRKS 576 Lambda K H 0.319 0.136 0.413 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: 984 Number of extensions: 33 Number of successful extensions: 2 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: 578 Length of database: 576 Length adjustment: 36 Effective length of query: 542 Effective length of database: 540 Effective search space: 292680 Effective search space used: 292680 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 (21.8 bits) S2: 53 (25.0 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