GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Azospirillum brasilense Sp245

Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate AZOBR_RS25270 AZOBR_RS25270 mandelate racemase

Query= SwissProt::Q1NAJ2
         (403 letters)



>FitnessBrowser__azobra:AZOBR_RS25270
          Length = 397

 Score =  175 bits (443), Expect = 2e-48
 Identities = 132/382 (34%), Positives = 191/382 (50%), Gaps = 35/382 (9%)

Query: 14  PGR--NFVTLKIMTDEGVYGLGDATLN-GRELAVASYLTDHVIPCLIGRDAHRIEDLWQY 70
           PGR  N + ++I T+ G+YG G+  +  G+E  VA+Y+ D + P LIGR+   I  L Q 
Sbjct: 13  PGRAKNLLFVRIETESGIYGWGEGYVTAGKEKVVAAYV-DAIAPLLIGREIWNIRQLAQT 71

Query: 71  LYKGAYWRRGPVT-MTAIAAVDMALWDIKGKIAGLPVYQLLGGASREGVMVYGHA---NG 126
           L      RR  V  + A++AV++A WDI GK AGLPV++LLGGA RE + VY +      
Sbjct: 72  LLDDFSIRRTSVDFLCALSAVEIASWDIVGKRAGLPVHKLLGGAVREKIRVYANGWWFGA 131

Query: 127 TTIEDTVKVALDYQAQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADADLPTENIWNTSK 186
           ++I+DT   A    AQGY A++    +PG    Y         +P D D   EN+     
Sbjct: 132 SSIDDTANRAAAVVAQGYDALKWD-PIPGPWRNY--------VDPKDLDHAVENV----- 177

Query: 187 YLRIVPELFKAARESLGWDVHLLHDIHHRLTPIEAGRLGQDLEPYRPFWLEDATPAENQE 246
                    +A RE++G +V LL D H RL+P  A RL + L  +   W E+  P EN +
Sbjct: 178 ---------RAVREAVGPNVELLIDGHRRLSPNHAIRLIERLREFGIAWYEEPCPPENLD 228

Query: 247 AFRLIRQHTTAPLAVGEIFNSIWDAKDLIQNQLIDYIRATVVHAGGITHLRRIAALADLY 306
               +R+ T  P+  GE   +      L + +  D I   +   GGI  +  IAALA  +
Sbjct: 229 LTAEVRRTTNVPIVSGEALYTKEQYLPLFEKRAADIINPDISAVGGILAMLDIAALAQPH 288

Query: 307 QIRTGCHGATDLSPVC-MAAALHFDLSVPNFGIQEYMRHMPE-TDAVFPHAYTFADGMMH 364
            I    H     SP+  +AA +H    V NF I E   ++ E T  +     T ADG + 
Sbjct: 289 SIAVSPHNFN--SPIVGLAATVHLSALVTNFTIAELFVNLVEPTRELALQGLTIADGYVD 346

Query: 365 PGDQPGLGVDIDEDLAAGYEYK 386
             D PGLGVD+D ++   + Y+
Sbjct: 347 IPDTPGLGVDLDVEVLRRHPYQ 368


Lambda     K      H
   0.322    0.139    0.438 

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: 406
Number of extensions: 25
Number of successful extensions: 5
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: 403
Length of database: 397
Length adjustment: 31
Effective length of query: 372
Effective length of database: 366
Effective search space:   136152
Effective search space used:   136152
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.

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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