GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Rhizobium etli CFN 42

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_011423489.1 RHE_RS00470 NAD-dependent succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_000092045.1:WP_011423489.1
          Length = 494

 Score =  347 bits (889), Expect = e-100
 Identities = 191/480 (39%), Positives = 275/480 (57%), Gaps = 20/480 (4%)

Query: 14  FIDGKFVPS-LDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +I+G + P     KTFD +NPAT E L ++ + GAAE   A+ AA  A    W    A E
Sbjct: 23  YINGVWTPGDAAAKTFDVLNPATGELLASLPDMGAAETRAAIDAAYAA-QPAWAARPAKE 81

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  +LRK  DLI+   + L+ + + + GKP         P A     + + YI     EA
Sbjct: 82  RSQILRKWFDLIVANADALAAILTAEMGKP--------FPEARGEILYAAAYIEWYAEEA 133

Query: 133 TQMDDVALN--------YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAE 184
            ++    +           I++PVGV+G I PWN P  ++  K+APALA G TVV KPAE
Sbjct: 134 KRIYGETIPAPSQDKRMIVIKQPVGVVGTITPWNFPAAMIARKIAPALAVGCTVVSKPAE 193

Query: 185 LTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIM 244
            TP+TA  LA +   AG+P GV NL+ G    + G  L  +  V  ISFTG T  G+I+M
Sbjct: 194 QTPLTAIALAVLAEQAGIPAGVFNLIVGLDGPAIGRELCGNDKVRKISFTGSTEVGRILM 253

Query: 245 ASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAY 304
              A  +K++S ELGG  P ++F D++LD  +E  + S + N G+ C+C +R+Y++   Y
Sbjct: 254 RQCADQIKKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYIQSGVY 313

Query: 305 EAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE 364
           +AF  K  AK  ++ VGD F    ++G LI ++   +V  ++  AV +G  ILTGGKR +
Sbjct: 314 DAFAAKLAAKVADMSVGDGFRPGVEIGPLIDEQGLAKVEDHVGDAVAKGAKILTGGKRID 373

Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424
           G   G F  PT++TG+TRD  V +EE FGPV  +  F+T E+V+ Q NDT +GL+A  + 
Sbjct: 374 G--AGTFFAPTVLTGVTRDMTVAREETFGPVAPLFRFETAEDVITQANDTEFGLAAYFYA 431

Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
            DL++  RVA  +E G+V +NT  +     PFGG+KQSG+GREG  H  + Y E+  +CI
Sbjct: 432 GDLKKVWRVAEALEYGMVGINTGLMSSEMAPFGGIKQSGLGREGSRHGADDYLEMKYLCI 491


Lambda     K      H
   0.318    0.136    0.404 

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: 607
Number of extensions: 27
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: 486
Length of database: 494
Length adjustment: 34
Effective length of query: 452
Effective length of database: 460
Effective search space:   207920
Effective search space used:   207920
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