GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Verminephrobacter eiseniae EF01-2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011811733.1 VEIS_RS19570 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_000015565.1:WP_011811733.1
          Length = 500

 Score =  535 bits (1379), Expect = e-156
 Identities = 267/480 (55%), Positives = 350/480 (72%), Gaps = 3/480 (0%)

Query: 46  LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105
           LL+ D  + GRW+     F V DPA+G KL  VA+ G  +A AA+ AA  A+  WK  + 
Sbjct: 16  LLKTDGLIDGRWVAGSRRFDVLDPATGLKLADVANLGPADADAAIAAANAAWGPWKSRTA 75

Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165
           KERS +LRKW +L++ ++D+LA+I+TAE GKPL EA+GE+ Y A F+EWF+EEA+R+ G+
Sbjct: 76  KERSIILRKWCELLLAHQDDLARIMTAEQGKPLAEAKGEVGYGASFVEWFAEEAKRINGE 135

Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225
            +      +R LVL+Q +GV + ITPWNFP AMITRKV  ALAAGC V++KPAE TP +A
Sbjct: 136 TLPQFDNSRRLLVLRQSIGVCAAITPWNFPLAMITRKVAPALAAGCPVIIKPAELTPLTA 195

Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285
           LA A+LA +AGIP GV+N++      +  +G+VLC   +V  ISFTGST  G+IL+  +A
Sbjct: 196 LAAAELALRAGIPAGVFNILCADGDNSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSA 255

Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345
            +VK++S+ELGG APFIVF  A++D AV GA ASK+RNAGQTCVC+NRF VQ  ++D FV
Sbjct: 256 PTVKKMSLELGGNAPFIVFADADIDSAVEGAFASKYRNAGQTCVCTNRFYVQEAVYDEFV 315

Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKR--HQS 403
            KFA A   + +VGNGF+ G  QGPLI E AV KV++HV DA+AKG  VVTGG+R  +  
Sbjct: 316 QKFA-AKVLTAKVGNGFDAGVNQGPLIEEAAVLKVQRHVADAIAKGGRVVTGGQRLPNLG 374

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
            G FFEPT+L++   DMLC  EETFGP AP+ KF  E+EA+A AN  + GLA YFYS+D 
Sbjct: 375 SGQFFEPTVLADARPDMLCAREETFGPFAPIFKFKTEQEAIAAANDTEFGLASYFYSRDL 434

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
            +I+RV E LE GMVGVN G++++   PFGGVKQSGLGREGS +GID+Y+E+KY+C G +
Sbjct: 435 GRIFRVGEALEYGMVGVNVGILATEHVPFGGVKQSGLGREGSHHGIDDYVEIKYLCLGDI 494


Lambda     K      H
   0.318    0.135    0.400 

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: 660
Number of extensions: 24
Number of successful extensions: 3
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: 523
Length of database: 500
Length adjustment: 35
Effective length of query: 488
Effective length of database: 465
Effective search space:   226920
Effective search space used:   226920
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 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