GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Desulfobacter vibrioformis DSM 8776

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q9S795
         (501 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  325 bits (832), Expect = 3e-93
 Identities = 184/477 (38%), Positives = 265/477 (55%), Gaps = 10/477 (2%)

Query: 11  FIDGEWREPILKKRIPIVNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGKDWAKAP 70
           FI  +W E   KK + + NPAT EV+G +P    ++   A++AA  +L       W    
Sbjct: 15  FIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA-----WRSKT 69

Query: 71  GAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLAEGLDA 130
            A R+  LR     + E + DLA L   + GKPL E+  ++   A  FE++A+ A+ +  
Sbjct: 70  AAQRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESRGEIAYAASFFEWFAEEAKRIYG 129

Query: 131 KQKAPVSLPMESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILKPSELA 190
                +   + S +  V+KQP+GVV  ITPWN+P  M   K   +LAAGCT ++KP+   
Sbjct: 130 DI---IPQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATAT 186

Query: 191 SVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSKVMTAA 250
             + L +A + +E G+PPGV NV+TG  S  G  L ++P V K+ FTGS   G K+M   
Sbjct: 187 PFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDC 246

Query: 251 AQLVKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHESIASEF 310
           A  +K VSMELGG +P IVFDD DLD A E AL   +  +GQ C   +RL V   +  +F
Sbjct: 247 AGTMKRVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQF 306

Query: 311 IEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGSRPEHLE 370
            EKL +    +K+ + +EEG   GP++     E + + I+ A  +GA +L GG R  H  
Sbjct: 307 CEKLARAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR--HAL 364

Query: 371 KGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHYGLGAAVISNDT 430
            G F  PT++ DVT  M + +EE+FGP   +  F SE E ++ AND+ YGL A   + D 
Sbjct: 365 GGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDM 424

Query: 431 ERCDRISEAFEAGIVWINCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTL 487
            R  R+ E  E G++ IN        AP+GGVK SG GRE  ++GLD+YL +K + +
Sbjct: 425 ARTWRVGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481


Lambda     K      H
   0.318    0.135    0.416 

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: 584
Number of extensions: 19
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: 501
Length of database: 485
Length adjustment: 34
Effective length of query: 467
Effective length of database: 451
Effective search space:   210617
Effective search space used:   210617
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: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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