Align D-galactonate dehydratase family member PC1_0802; EC 4.2.1.-; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate BWI76_RS15895 BWI76_RS15895 starvation-sensing protein RspA
Query= curated2:C6D9S0 (404 letters) >FitnessBrowser__Koxy:BWI76_RS15895 Length = 404 Score = 806 bits (2081), Expect = 0.0 Identities = 376/404 (93%), Positives = 392/404 (97%) Query: 1 MKIVSAEVFVTCPGRNFVTLKITTDSGLTGLGDATLNGRELPVASYLNDHVCPQLIGRDA 60 MKIV+AEVFVTCPGRNFVTLK+TTD G+ GLGDATLNGREL VASYL DH+CPQLIGRDA Sbjct: 1 MKIVAAEVFVTCPGRNFVTLKVTTDDGIVGLGDATLNGRELSVASYLRDHLCPQLIGRDA 60 Query: 61 HQIEDIWQYFYKGAYWRRGPVTMSAISAVDMALWDIKAKAANMPLYQLLGGASRTGVMVY 120 H+IEDIWQ+FYKGAYWRRGPVTMSAISA+DMALWDIKAKAA MPLYQLLGGASR GVMVY Sbjct: 61 HRIEDIWQFFYKGAYWRRGPVTMSAISAIDMALWDIKAKAAGMPLYQLLGGASREGVMVY 120 Query: 121 CHTTGHSIDEVLDDYAKHRDQGFKAIRVQCGVPGMETTYGMAKGKGLAYEPATKGSLPEE 180 CHTTGHSIDEVLDDYA+H++ GFKAIRVQCGVPGM+TTYGMAKGKG AYEPATKG PEE Sbjct: 121 CHTTGHSIDEVLDDYARHKEMGFKAIRVQCGVPGMKTTYGMAKGKGQAYEPATKGQWPEE 180 Query: 181 QLWSTEKYLDFTPKLFEAVRDKFGFNEHLLHDMHHRLTPIEAARFGKSVEDYRLFWMEDP 240 QLWSTEKYLDFTP+LF AVR+KFGFNEHLLHDMHHRLTPIEAARFGKS+EDYRLFWMEDP Sbjct: 181 QLWSTEKYLDFTPQLFAAVREKFGFNEHLLHDMHHRLTPIEAARFGKSIEDYRLFWMEDP 240 Query: 241 TPAENQACFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRI 300 TPAENQ CFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRI Sbjct: 241 TPAENQECFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRI 300 Query: 301 ADFASLYQVRTGSHGPSDLSPICMAAALHFDLWVPNFGVQEYMGYSEQMLEVFPHSWTFD 360 ADFASLYQVRTGSHGPSDLSP+CMAAALHFDLWVPNFGVQEYMGYSEQMLEVFPHSWTFD Sbjct: 301 ADFASLYQVRTGSHGPSDLSPVCMAAALHFDLWVPNFGVQEYMGYSEQMLEVFPHSWTFD 360 Query: 361 NGYMHPGEKPGLGIEFDEKLAAKYPYDPAYLPVARLEDGTLWNW 404 NGYMHPGEKPGLGIEFDEKLAAKYPY+PAYLPVARLEDGTLWNW Sbjct: 361 NGYMHPGEKPGLGIEFDEKLAAKYPYEPAYLPVARLEDGTLWNW 404 Lambda K H 0.321 0.138 0.442 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: 779 Number of extensions: 27 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: 404 Length of database: 404 Length adjustment: 31 Effective length of query: 373 Effective length of database: 373 Effective search space: 139129 Effective search space used: 139129 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 (21.9 bits) S2: 50 (23.9 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