GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Rhizobium etli CFN 42

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011427659.1 RHE_RS23010 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_000092045.1:WP_011427659.1
          Length = 484

 Score =  511 bits (1315), Expect = e-149
 Identities = 254/473 (53%), Positives = 339/473 (71%), Gaps = 6/473 (1%)

Query: 53  VGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSS 110
           +  RW+     A+  V +PA+G  LG+V D G  E   A+ AA  A   W + +  ER++
Sbjct: 15  IADRWIEAEGRASAMVRNPATGEVLGSVPDFGAAETEEAIAAAVVAQKLWAKKTAGERAT 74

Query: 111 LLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTS 170
           +L+ W+ LMI+N+D+LA I+T E GKPL EA+GEI Y A F+EWF+EEARR+ G+I+   
Sbjct: 75  VLKTWHRLMIENRDDLAMILTLEQGKPLAEAKGEITYGASFIEWFAEEARRINGEIVPGH 134

Query: 171 AKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQ 230
             DKR LVL+QP GV + ITPWNFP+AMITRK+G ALAAGC VV+KPA  TP+SA+A+A 
Sbjct: 135 QPDKRILVLRQPAGVVAAITPWNFPNAMITRKIGPALAAGCAVVLKPALQTPFSAIAIAV 194

Query: 231 LANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKR 290
           LA +AG+P G+ N++      A  +G  L     V  ++FTGST TG++L    A ++K+
Sbjct: 195 LAERAGLPAGLLNIVTGD---AAAIGGALTASRDVRVLTFTGSTRTGELLYRQCAPTIKK 251

Query: 291 VSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAE 350
           + +ELGG APFIVFD A++D AV GA+ +KFRN GQTCVC+NR  VQ G++++F  K AE
Sbjct: 252 LGLELGGNAPFIVFDDADLDAAVEGAIIAKFRNNGQTCVCANRLYVQDGVYEAFAAKLAE 311

Query: 351 AMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFEP 410
           A+ K L+VGNG E     GPLI++ AV KVE H+ DAVAKGA +VTGGKRH  GG+FFEP
Sbjct: 312 AVSK-LKVGNGLERDVVLGPLIDDNAVAKVESHIQDAVAKGAGIVTGGKRHALGGHFFEP 370

Query: 411 TLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRVA 470
           T+L +V   M    EETFGP+AP+ +F  E++ +  AN  + GLA YFY++D ++++RVA
Sbjct: 371 TILRDVAAGMQVAREETFGPLAPLFRFRDEQDVIEQANDTEFGLASYFYARDLSRVFRVA 430

Query: 471 EQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
           E LE GMVGVN GL+S+ E PFGGVK SGLGREGS++G+DEY E+KYVC GG+
Sbjct: 431 EALEYGMVGVNTGLVSTAEAPFGGVKMSGLGREGSRHGLDEYTELKYVCLGGI 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: 629
Number of extensions: 22
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 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