Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BWI76_RS15895 BWI76_RS15895 starvation-sensing protein RspA
Query= BRENDA::D4GP40 (412 letters) >FitnessBrowser__Koxy:BWI76_RS15895 Length = 404 Score = 151 bits (382), Expect = 3e-41 Identities = 114/374 (30%), Positives = 176/374 (47%), Gaps = 44/374 (11%) Query: 52 WILVRVYTDAGVVGTGEAYWGGGDTAIIERMK----PFLVGENPLDIDRLYEHLVQKMSG 107 ++ ++V TD G+VG G+A G + ++ ++ P L+G + I+ +++ + G Sbjct: 17 FVTLKVTTDDGIVGLGDATLNGRELSVASYLRDHLCPQLIGRDAHRIEDIWQFFYK---G 73 Query: 108 EGSVSGKV-ISAISGIEIALHDVAGKLLDVPAYQLVGGKYRDEVRVYCDL--HTEDEANP 164 G V +SAIS I++AL D+ K +P YQL+GG R+ V VYC H+ DE Sbjct: 74 AYWRRGPVTMSAISAIDMALWDIKAKAAGMPLYQLLGGASREGVMVYCHTTGHSIDEVLD 133 Query: 165 QACAEEGVRVVEELGYDAIKFDLDVPS-----GHEKDRANRHL-----RNPE-------- 206 + E+G+ AI+ VP G K + + + PE Sbjct: 134 DYARHK------EMGFKAIRVQCGVPGMKTTYGMAKGKGQAYEPATKGQWPEEQLWSTEK 187 Query: 207 -IDHKVEIVEAVTEAVGDRADVAFDCHWSFTGGSAKRLASELEDYDVWWLEDPVPPENHD 265 +D ++ AV E G + D H T A R +EDY ++W+EDP P EN + Sbjct: 188 YLDFTPQLFAAVREKFGFNEHLLHDMHHRLTPIEAARFGKSIEDYRLFWMEDPTPAENQE 247 Query: 266 VQKLVTQSTTTPIAVGENVYRKFGQRTLLEPQAVDIIAPDLPRVGGMRETRKIADLADMY 325 +L+ Q T TPIAVGE + + L+E Q +D I + GG+ R+IAD A +Y Sbjct: 248 CFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRIADFASLY 307 Query: 326 YIPVAMHNVS--SPIGTMASAQVAAAIPNSLALEYHSYQLGWWEDLVE---EDDLIQNGH 380 + H S SP+ A+ +PN EY +G+ E ++E NG+ Sbjct: 308 QVRTGSHGPSDLSPVCMAAALHFDLWVPNFGVQEY----MGYSEQMLEVFPHSWTFDNGY 363 Query: 381 MEIPEKPGLGLTLD 394 M EKPGLG+ D Sbjct: 364 MHPGEKPGLGIEFD 377 Lambda K H 0.315 0.135 0.401 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: 426 Number of extensions: 27 Number of successful extensions: 4 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: 412 Length of database: 404 Length adjustment: 31 Effective length of query: 381 Effective length of database: 373 Effective search space: 142113 Effective search space used: 142113 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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