Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 7024896 Shewana3_2070 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::ANA3:7024896 (586 letters) >FitnessBrowser__ANA3:7024896 Length = 586 Score = 1182 bits (3058), Expect = 0.0 Identities = 586/586 (100%), Positives = 586/586 (100%) Query: 1 MCLGRRRCHMNNKKPKTLRSASWFGSDDKNGFMYRSWMKNQGIPEHHFQNKPVIGICNTW 60 MCLGRRRCHMNNKKPKTLRSASWFGSDDKNGFMYRSWMKNQGIPEHHFQNKPVIGICNTW Sbjct: 1 MCLGRRRCHMNNKKPKTLRSASWFGSDDKNGFMYRSWMKNQGIPEHHFQNKPVIGICNTW 60 Query: 61 SELTPCNGHLRELAQRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAI 120 SELTPCNGHLRELAQRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAI Sbjct: 61 SELTPCNGHLRELAQRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAI 120 Query: 121 RGNPIDGVVLLVGCDKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELH 180 RGNPIDGVVLLVGCDKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELH Sbjct: 121 RGNPIDGVVLLVGCDKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELH 180 Query: 181 QEYKAGNISLAAFMNAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRR 240 QEYKAGNISLAAFMNAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRR Sbjct: 181 QEYKAGNISLAAFMNAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRR 240 Query: 241 QVLAHMSGMRIVDMVKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVE 300 QVLAHMSGMRIVDMVKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVE Sbjct: 241 QVLAHMSGMRIVDMVKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVE 300 Query: 301 LSLDDWRHGYTVPTIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASL 360 LSLDDWRHGYTVPTIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASL Sbjct: 301 LSLDDWRHGYTVPTIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASL 360 Query: 361 WDNVKEAPCYNQEVIMSLENPLVENGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVV 420 WDNVKEAPCYNQEVIMSLENPLVENGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVV Sbjct: 361 WDNVKEAPCYNQEVIMSLENPLVENGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVV 420 Query: 421 FESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKDMVRI 480 FESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKDMVRI Sbjct: 421 FESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKDMVRI 480 Query: 481 SDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLAK 540 SDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLAK Sbjct: 481 SDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLAK 540 Query: 541 LATVKSIPVNGGYLSLFKEHVLQADEGCDFDFLVGCRGAEIPAHSH 586 LATVKSIPVNGGYLSLFKEHVLQADEGCDFDFLVGCRGAEIPAHSH Sbjct: 541 LATVKSIPVNGGYLSLFKEHVLQADEGCDFDFLVGCRGAEIPAHSH 586 Lambda K H 0.318 0.135 0.403 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: 1301 Number of extensions: 35 Number of successful extensions: 1 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: 586 Length of database: 586 Length adjustment: 37 Effective length of query: 549 Effective length of database: 549 Effective search space: 301401 Effective search space used: 301401 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 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