GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF2064 HP15_2020 succinate-semialdehyde
           dehydrogenase I
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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