GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Rhodanobacter denitrificans 2APBS1

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_015447966.1 R2APBS1_RS10710 aldehyde dehydrogenase

Query= metacyc::MONOMER-13361
         (500 letters)



>NCBI__GCF_000230695.2:WP_015447966.1
          Length = 476

 Score =  213 bits (543), Expect = 9e-60
 Identities = 149/455 (32%), Positives = 228/455 (50%), Gaps = 19/455 (4%)

Query: 42  NGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEFVAA 101
           +G+L + V   DAK V +A+ AA NA K P  +     R  ++   A     R +E   A
Sbjct: 28  SGRLATRVAVPDAKAVEKAIAAAVNAAK-PMREFKPWARQTVLQYCAARFAERRDELAEA 86

Query: 102 EVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDG-SGALNYTVRKPLG 160
              + G+P+  A   ++ R I  FR  A+ A   + +   +  +    G   YT R PLG
Sbjct: 87  LCIEAGKPIKDAAG-EVTRLIETFRIAAEEAVRINGETINLELASRLDGYHGYTRRVPLG 145

Query: 161 VIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVFNL 220
            +  I+P+N PL L   KVAPA+A G   V KPSE++P  A ++ EV+ +  +P G F++
Sbjct: 146 PVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPSEKTPIGALIIGEVLAETDLPKGAFSI 205

Query: 221 IHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVFAD 280
           +   G  +A   L + P    L+FTG     +   +A   G K+V+ ELGG  A +V AD
Sbjct: 206 LTLDGAHAAP--LVEDPRFKLLSFTGGQVGWALKARA---GHKKVTLELGGNAACIVDAD 260

Query: 281 AD--LDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQDG 338
            D  LD  ++ ++  +F  SGQ C+  +R+Y H  I+D     L    ++L  G P    
Sbjct: 261 QDGKLDHVVQRLVFGAFYQSGQSCIGVQRIYAHADIYDALKRKLVAATKKLKAGDPKDRS 320

Query: 339 VNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSDKA 398
           V +GP+I     +++  +   A   G  ++ GG        +  G  +  T+   +   A
Sbjct: 321 VFLGPMIDEAAAERLHGWILEAKQAGGRILCGG--------KRHGNMLDATLMENVPADA 372

Query: 399 RCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLVWV 458
           +    E FGP   ++PF   DE I  VNDS+YGL   I+T +L+ A R   ++  G V V
Sbjct: 373 KANRMEAFGPFALLAPFRRFDEAIAMVNDSDYGLQAGIFTDSLAHAMRAWNELEQGGVIV 432

Query: 459 NTW-YLRDLRTPFGGVKLSGLGREGGRFSMDFYSD 492
           N     R    P+GGVKLSGLGREG R++++  S+
Sbjct: 433 NDIPSFRVDNMPYGGVKLSGLGREGVRYAIEDMSE 467


Lambda     K      H
   0.318    0.135    0.405 

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: 528
Number of extensions: 14
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: 500
Length of database: 476
Length adjustment: 34
Effective length of query: 466
Effective length of database: 442
Effective search space:   205972
Effective search space used:   205972
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 24 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