GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Klebsiella michiganensis M5al

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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