GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sinorhizobium meliloti 1021

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate SMc02780 SMc02780 succinate-semialdehyde dehydrogenase [NADP+] protein

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__Smeli:SMc02780
          Length = 484

 Score =  531 bits (1367), Expect = e-155
 Identities = 262/480 (54%), Positives = 352/480 (73%), Gaps = 6/480 (1%)

Query: 46  LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           L R  + VG  W+         V +PA+G  +G V   G  + R A+ AA      W   
Sbjct: 8   LFRQAALVGETWIEADPKNAIEVNNPATGEIIGRVPKLGAADTRTAIEAAARVQKEWAAR 67

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KERS++LR+W++LMI+NKD+L +I+T E GKPL EA GEI+Y A F+EWF+EEARRVY
Sbjct: 68  TAKERSAVLRRWFELMIENKDDLGRILTMEQGKPLAEATGEIVYGASFIEWFAEEARRVY 127

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD++    KDKR LV+KQP+GV + ITPWNFP+AMITRK G ALAAGC +V+KPA  TP+
Sbjct: 128 GDLVPGHQKDKRILVMKQPIGVVAAITPWNFPNAMITRKAGPALAAGCAMVLKPAAQTPF 187

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SA+A+A LA +AG+P G+++VI  S   A+E+G  + ++P V K++FTGST  G  L   
Sbjct: 188 SAIAIAVLAERAGMPKGLFSVITGS---AREIGAEMTSNPTVRKLTFTGSTEVGAELYRQ 244

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
           +A ++K++ +ELGG APFIVFD A++D AV GA+ +KFRN GQTCVC+NR  VQ G++++
Sbjct: 245 SAATIKKLGLELGGNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRIYVQDGVYEA 304

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K A+A+ K L+ GNG E+G   GPLI++ A++KVE+HV DA+AKGA VV GG+RH  
Sbjct: 305 FSDKLAQAVAK-LKTGNGMEDGVILGPLIDQPALKKVEEHVADALAKGARVVQGGRRHSL 363

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           GG F+E T+L++VT+ M    EETFGPVAP+ +F  E + +A AN  + GLA YFY++D 
Sbjct: 364 GGTFYEATVLADVTQAMAVAREETFGPVAPLFRFKDESDVIAQANDTEFGLASYFYAKDL 423

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
           A+++RVAE LE GMVGVN GLIS+ E PFGGVK SGLGREGSKYGI+E++E+KYVC GG+
Sbjct: 424 ARVFRVAEALEYGMVGVNTGLISTAEAPFGGVKLSGLGREGSKYGIEEFMEIKYVCLGGI 483


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: 633
Number of extensions: 23
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: 484
Length adjustment: 34
Effective length of query: 489
Effective length of database: 450
Effective search space:   220050
Effective search space used:   220050
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 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