Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate BWI76_RS15895 BWI76_RS15895 starvation-sensing protein RspA
Query= BRENDA::G3Y8T6 (383 letters) >FitnessBrowser__Koxy:BWI76_RS15895 Length = 404 Score = 175 bits (443), Expect = 2e-48 Identities = 129/396 (32%), Positives = 190/396 (47%), Gaps = 46/396 (11%) Query: 4 IKSIEYFRVKPRWLFV--KVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADD 60 I + E F P FV KVT + G G+ATL G +V L D + +++G +A Sbjct: 3 IVAAEVFVTCPGRNFVTLKVTTDDGIVGLGDATLNGRELSVASYLRDHLCPQLIGRDAHR 62 Query: 61 IEHVWQTIWRLGFYRGGPVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAW 120 IE +WQ ++ ++R GPV MSA+S ID+ALWD+K + +P+YQLLGG R V VY Sbjct: 63 IEDIWQFFYKGAYWRRGPVTMSAISAIDMALWDIKAKAAGMPLYQLLGGASREGVMVYCH 122 Query: 121 IGGDRPSDV--------EVAAKARIAQ----GLK---------------CVKMNATEDMN 153 G +V E+ KA Q G+K K E+ Sbjct: 123 TTGHSIDEVLDDYARHKEMGFKAIRVQCGVPGMKTTYGMAKGKGQAYEPATKGQWPEEQL 182 Query: 154 WLDSPSVLDSCIERIKQVKA-LGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPL 210 W + LD + V+ G + L D H RL A + K++E YR ++E+P Sbjct: 183 W-STEKYLDFTPQLFAAVREKFGFNEHLLHDMHHRLTPIEAARFGKSIEDYRLFWMEDPT 241 Query: 211 LVEHPEAIKQLSQHTTIPIAFGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIA 270 E+ E + + QHT PIA GE + WD K+ +E+ +D ++ I HAGGI+ +RIA Sbjct: 242 PAENQECFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRIA 301 Query: 271 TMAETYDVAIAPHCP--LGPIALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYL 328 A Y V H P L P+ +AA++ L PNF +QE M Y+ + ++ Sbjct: 302 DFASLYQVRTGSHGPSDLSPVCMAAALHFDLWVPNFGVQEY---MGYSEQMLEV------ 352 Query: 329 TNPTVFNIEEGYVPAPTGAGLGVEIDEELVRRISRE 364 P + + GY+ GLG+E DE+L + E Sbjct: 353 -FPHSWTFDNGYMHPGEKPGLGIEFDEKLAAKYPYE 387 Lambda K H 0.320 0.138 0.425 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: 423 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 404 Length adjustment: 31 Effective length of query: 352 Effective length of database: 373 Effective search space: 131296 Effective search space used: 131296 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: 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