GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas fluorescens GW456-L13

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate PfGW456L13_3604 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= curated2:Q1QTQ7
         (489 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604
          Length = 490

 Score =  194 bits (493), Expect = 6e-54
 Identities = 152/461 (32%), Positives = 230/461 (49%), Gaps = 17/461 (3%)

Query: 4   KQQLLIDGAWVDGDAARFAKT-DPVSGETLWTATAASATQVEHAVAAARQAFPD-WARRS 61
           + QL I+G WV  D   +    DP + +      A +   V+HAV AAR+AF + W + S
Sbjct: 2   RDQLYINGEWVSPDLGGYLDVIDPATEQAFHRVAAGTEEDVDHAVRAARRAFDNGWGQTS 61

Query: 62  FAERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIG--KVAISITAYHER 119
            AER   +E   + LE+ ++ LA    ++ GKPL EA+ ++G  I   +    +    ++
Sbjct: 62  GAERGQWLEALADELESGQQALAELEVRDNGKPLPEAQWDIGDAIACFRYYAGLARELDQ 121

Query: 120 TGERARDIGDARAV--LRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQT 177
             ++   + DAR    +RH P GV     P+N+P  +    + PAL AG  VV KPSE T
Sbjct: 122 QQDQPLALPDARFCCRIRHEPIGVAGQIIPWNYPLLMAAWKVAPALAAGATVVLKPSELT 181

Query: 178 PMTADLTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLLHRQF 236
           P+TA          GLPAGV+NLV G  A+ G  L     +D L FTGS   G  +    
Sbjct: 182 PLTALELAAAADRIGLPAGVLNLVTGLGADAGSPLTEHPGVDKLAFTGSVPTGAKIMSAA 241

Query: 237 GGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGD 296
              + K ++LELGG +  +V D  D EAAV  IL   F + GQ C+   RL+V    +  
Sbjct: 242 ARDI-KNISLELGGKSAFIVFDDADVEAAVEWILFGIFWNQGQVCSATSRLLVQE-TIAA 299

Query: 297 DLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRR-- 354
            LI+ L     ++ +  P  +P      L S    D +L   D  +A G R L+  RR  
Sbjct: 300 RLIERLVEETRKISI-GPGMQPGVLLGPLVSQGQYDKVLGFIDQGLASGARLLTGGRRPA 358

Query: 355 -LQAGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLI 411
            L+ G   + P + D  G    +  EE FGP+L + R++  ++A+ +AN +R+GL+A ++
Sbjct: 359 HLREG-YFVEPAIFDEPGHSSILWREEVFGPVLCIKRFKTEEQALQMANASRFGLAAAVM 417

Query: 412 GGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSG 452
             +         ++RAGIV W   +     +AP+GG+  SG
Sbjct: 418 SADLQRTARVANQLRAGIV-WVNCSQPTFVEAPWGGMKHSG 457


Lambda     K      H
   0.319    0.135    0.409 

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: 639
Number of extensions: 30
Number of successful extensions: 6
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: 489
Length of database: 490
Length adjustment: 34
Effective length of query: 455
Effective length of database: 456
Effective search space:   207480
Effective search space used:   207480
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: 52 (24.6 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