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_011423489.1 RHE_RS00470 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_000092045.1:WP_011423489.1
          Length = 494

 Score =  543 bits (1398), Expect = e-159
 Identities = 270/481 (56%), Positives = 345/481 (71%), Gaps = 6/481 (1%)

Query: 46  LLRGDSFVGGRWLPTPA---TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102
           LLR   ++ G W P  A   TF V +PA+G  L ++ D G  E RAA+ AAY A  +W  
Sbjct: 17  LLRDAGYINGVWTPGDAAAKTFDVLNPATGELLASLPDMGAAETRAAIDAAYAAQPAWAA 76

Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162
              KERS +LRKW+DL++ N D LA I+TAE GKP  EA+GEILY+A ++EW++EEA+R+
Sbjct: 77  RPAKERSQILRKWFDLIVANADALAAILTAEMGKPFPEARGEILYAAAYIEWYAEEAKRI 136

Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222
           YG+ I   ++DKR +V+KQPVGV   ITPWNFP+AMI RK+  ALA GCTVV KPAE TP
Sbjct: 137 YGETIPAPSQDKRMIVIKQPVGVVGTITPWNFPAAMIARKIAPALAVGCTVVSKPAEQTP 196

Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282
            +A+ALA LA QAGIP GV+N+I         +G  LC +  V KISFTGST  G+IL+ 
Sbjct: 197 LTAIALAVLAEQAGIPAGVFNLI--VGLDGPAIGRELCGNDKVRKISFTGSTEVGRILMR 254

Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342
             A+ +K+VS+ELGG APFIVFD A++D AV GA+ASK+RNAGQTCVC+NR  +Q G++D
Sbjct: 255 QCADQIKKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYIQSGVYD 314

Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402
           +F  K A A    + VG+GF  G   GPLI+E+ + KVE HV DAVAKGA ++TGGKR  
Sbjct: 315 AFAAKLA-AKVADMSVGDGFRPGVEIGPLIDEQGLAKVEDHVGDAVAKGAKILTGGKRID 373

Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462
             G FF PT+L+ VTRDM    EETFGPVAP+ +F+  E+ +  AN  + GLA YFY+ D
Sbjct: 374 GAGTFFAPTVLTGVTRDMTVAREETFGPVAPLFRFETAEDVITQANDTEFGLAAYFYAGD 433

Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522
             ++WRVAE LE GMVG+N GL+SS   PFGG+KQSGLGREGS++G D+YLE+KY+C GG
Sbjct: 434 LKKVWRVAEALEYGMVGINTGLMSSEMAPFGGIKQSGLGREGSRHGADDYLEMKYLCIGG 493

Query: 523 L 523
           L
Sbjct: 494 L 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: 685
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: 523
Length of database: 494
Length adjustment: 34
Effective length of query: 489
Effective length of database: 460
Effective search space:   224940
Effective search space used:   224940
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