GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas putida KT2440

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PP_0213 PP_0213 succinate-semialdehyde dehydrogenase (NADP+)

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__Putida:PP_0213
          Length = 480

 Score =  249 bits (636), Expect = 2e-70
 Identities = 159/475 (33%), Positives = 232/475 (48%), Gaps = 25/475 (5%)

Query: 41  YIGGEWVDTKE-RMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRS 99
           YI GEW+D    + + +   A  EV+GT  K G AE   A+EAA KA   W+    ++RS
Sbjct: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73

Query: 100 RLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEV 159
             L +   LM   + +L   +  E GK   EA  ++A A  FIE++A  A R     +  
Sbjct: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTI-- 131

Query: 160 VPYPGEDNESFYV----PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVV 215
              PG   +   +    P+G    I PWNFP A+ T      +A G T++ KPA      
Sbjct: 132 ---PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYS 188

Query: 216 GAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRL 275
              + E+ H AG P GV++ + G   EVG  L  +   R ++FTGS E+G ++ E   + 
Sbjct: 189 ALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK- 247

Query: 276 APGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAY 335
                  K+  +E GG    IV + AD D A EG ++S Y   GQ C  A+R+ +  G Y
Sbjct: 248 -----DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVY 302

Query: 336 EPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEG 394
           +   E++     +L +G   EE    GP++  +   KV  +IE   ++G  VL G +L  
Sbjct: 303 DAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI- 361

Query: 395 EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKR 454
           EG F  PT+  +VP  A +A+EE FGP+  + R KD AE + ++NDT +GL    Y+R  
Sbjct: 362 EGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDM 421

Query: 455 EHLEWARREFHVGNLYFNRKITGALVG-VQPFGGFKLSG---TNAKTGALDYLRL 505
             +         G +  N   TG +   V PFGG K SG     +K G  DYL +
Sbjct: 422 SRVFRVAEALEYGMVGIN---TGLISNEVAPFGGIKASGLGREGSKYGIEDYLEI 473


Lambda     K      H
   0.319    0.137    0.403 

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: 553
Number of extensions: 32
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: 516
Length of database: 480
Length adjustment: 34
Effective length of query: 482
Effective length of database: 446
Effective search space:   214972
Effective search space used:   214972
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 (21.7 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