GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Marinobacter adhaerens HP15

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__Marino:GFF2064
          Length = 489

 Score =  572 bits (1473), Expect = e-167
 Identities = 272/481 (56%), Positives = 369/481 (76%), Gaps = 3/481 (0%)

Query: 45  DLLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102
           +LLR  +++ G+W+   +  TF V DPA+G +L TV D    +ARAA+ AA  A+ +W+ 
Sbjct: 9   ELLREQAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRS 68

Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162
              KER+++LRKW++L++ N+++LA+++TAE GKPL E++GE+ Y A F+EWF+EEA+R 
Sbjct: 69  TPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRA 128

Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222
           YGD+I    KDKR +V+KQPVGV + ITPWNFP AMITRKV  ALAAGC VVVKPAEDTP
Sbjct: 129 YGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTP 188

Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282
            SALA+  LA +AG+P G+ N+I CS+  A  VG  L  +P+V K+SFTGST  GK+L+ 
Sbjct: 189 LSALAITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGKLLMR 248

Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342
            A+++VK+VS+ELGG APFIVFD A++D AVAG MASK+RN GQTCVC+NR  VQ G++D
Sbjct: 249 QASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQAGVYD 308

Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402
           +F  K   A+ K + VG G E  T QGPLIN+ A+ KV++H+ DA +KGA V  GG+ H 
Sbjct: 309 AFAEKLKAAVSKMV-VGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGRAHS 367

Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462
            GG FFEPT+L++ T++ML   EETFGPVAP+ KF+ ++EA+A+AN ++ GL+ YFYS++
Sbjct: 368 LGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFYSRN 427

Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522
             ++WRVAE+LE GM+GVNEG+IS+   PFGGVK+SGLGREGS YG+DEY+E+KY+C GG
Sbjct: 428 IHRVWRVAEELESGMIGVNEGIISTEVAPFGGVKESGLGREGSHYGLDEYMELKYLCLGG 487

Query: 523 L 523
           +
Sbjct: 488 M 488


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: 688
Number of extensions: 23
Number of successful extensions: 2
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: 489
Length adjustment: 34
Effective length of query: 489
Effective length of database: 455
Effective search space:   222495
Effective search space used:   222495
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.

Links

Downloads

Related tools

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