GapMind for catabolism of small carbon sources

 

Alignments for a candidate for man-isomerase in Cupriavidus basilensis 4G11

Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate RR42_RS28130 RR42_RS28130 N-acylglucosamine 2-epimerase

Query= reanno::acidovorax_3H11:Ac3H11_2078
         (424 letters)



>FitnessBrowser__Cup4G11:RR42_RS28130
          Length = 379

 Score = 72.4 bits (176), Expect = 2e-17
 Identities = 78/261 (29%), Positives = 101/261 (38%), Gaps = 28/261 (10%)

Query: 92  FLDPATGGYAWLIDWQDGRATVQDTTRHCYGMAFVMLAYARAYE-AGVPEARVWLAEAFD 150
           F D   GG+ + ID Q       DTT+  Y  AFV+ A A  ++ +G  +AR  L  A  
Sbjct: 98  FADGGQGGFIYSIDAQ---GQPLDTTKDLYTHAFVVFACAAYFKRSGSAQARALLDGATR 154

Query: 151 TAEQHFWQPAAGLYADEASPDWQ-LTSYRGQNANMHACEAMISAFRATGERRYIERAEQL 209
             E  F   A GLY    + D++ L     QN  MH  EA ++AF  TGER Y +R   +
Sbjct: 155 LIEARF-ATADGLYHAALAQDFRPLGGPPQQNPIMHLTEAYLAAFEVTGERFYADRLAGI 213

Query: 210 AQGICQRQAALSDRTHAPAAEGWVWEHFHADWSVDWDYNRHDRSNIFRPWGYQVGHQTEW 269
           A  +          T    A G + E        D   NR            + GHQ EW
Sbjct: 214 AAAVLA--------TFVDPATGCIAE---LPMCTDRAGNR-----------VEPGHQFEW 251

Query: 270 AKLLLQLDALLPADWHLPCAQRLFDTAVERGWDAEHGGLYYGMAPDGSICDDGKYHWVQA 329
             LL    AL           R F  A++ G D    G+   +  DGS  D  +  W Q 
Sbjct: 252 FSLLASAPALFEDSGLAQALARAFGFAMQHGVDTSTMGVAAALHLDGSPRDPIQRIWAQT 311

Query: 330 ESMAAAAVLAVRTGDARYWQW 350
           E   A AV       A    W
Sbjct: 312 EFARALAVRGDSVALAHLQAW 332



 Score = 27.7 bits (60), Expect = 6e-04
 Identities = 36/144 (25%), Positives = 55/144 (38%), Gaps = 19/144 (13%)

Query: 69  YRTTGEARYQVGMRHALEFLRTAFLDPATGGYAWLIDWQDGRATVQDTTRHCYGMAFVML 128
           +  TGE  Y   +      +   F+DPATG  A L    D      +        + +  
Sbjct: 198 FEVTGERFYADRLAGIAAAVLATFVDPATGCIAELPMCTDRAGNRVEPGHQFEWFSLLAS 257

Query: 129 AYARAYEAGVPEARVWLAEAFDTAEQH-----FWQPAAGLYADEASPD-----WQLTSY- 177
           A A   ++G+ +A   LA AF  A QH         AA L+ D +  D     W  T + 
Sbjct: 258 APALFEDSGLAQA---LARAFGFAMQHGVDTSTMGVAAALHLDGSPRDPIQRIWAQTEFA 314

Query: 178 -----RGQNANMHACEAMISAFRA 196
                RG +  +   +A + A+ A
Sbjct: 315 RALAVRGDSVALAHLQAWLKAYPA 338



 Score = 25.4 bits (54), Expect = 0.003
 Identities = 18/58 (31%), Positives = 24/58 (41%)

Query: 289 AQRLFDTAVERGWDAEHGGLYYGMAPDGSICDDGKYHWVQAESMAAAAVLAVRTGDAR 346
           A RLF +   R  D   GG  Y +   G   D  K  +  A  + A A    R+G A+
Sbjct: 87  AARLFASLGGRFADGGQGGFIYSIDAQGQPLDTTKDLYTHAFVVFACAAYFKRSGSAQ 144


Lambda     K      H
   0.324    0.135    0.460 

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: 484
Number of extensions: 28
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 424
Length of database: 379
Length adjustment: 31
Effective length of query: 393
Effective length of database: 348
Effective search space:   136764
Effective search space used:   136764
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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