GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Marinobacter adhaerens HP15

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Marino:GFF2064
          Length = 489

 Score =  348 bits (894), Expect = e-100
 Identities = 190/468 (40%), Positives = 265/468 (56%), Gaps = 3/468 (0%)

Query: 10  QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69
           Q  I+G+W+ A SGKT  V +PA G+ +  V      D   A+ AA + + AWR  PA E
Sbjct: 14  QAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRSTPAKE 73

Query: 70  RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129
           RA  +RK   L+    + +A+LMT EQGKPL E+R EV   A  IEWFA+E +R YG ++
Sbjct: 74  RANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRAYGDVI 133

Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189
           P      +  V+K+PVG VAA TPWNFP+  + RK++ ALA GC  +VK  E+TP S  A
Sbjct: 134 PGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTPLSALA 193

Query: 190 LLRAFVDAGVPAGVIGLVY---GDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLH 246
           +     +AGVPAG+I ++     +   + S L  +P++RKV+FTGSTPVGK L   A   
Sbjct: 194 ITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGKLLMRQASDT 253

Query: 247 MKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRA 306
           +K+ ++ELGG+AP IV +DAD+  AV     +K+RN GQ C+   R  V   + D F   
Sbjct: 254 VKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQAGVYDAFAEK 313

Query: 307 LVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFF 366
           L      + VG GLE  T  G L N   L  +   I++A   GA +  GG      G FF
Sbjct: 314 LKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGRAHSLGGTFF 373

Query: 367 APTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHL 426
            PT++ +   +  +   E FGPVA +  F+  +EAIA AN   FGL+ Y ++R+   V  
Sbjct: 374 EPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFYSRNIHRVWR 433

Query: 427 LTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
           + + LE GM+ +N+        PFGGVK+SG G EG    L+ Y+  K
Sbjct: 434 VAEELESGMIGVNEGIISTEVAPFGGVKESGLGREGSHYGLDEYMELK 481


Lambda     K      H
   0.318    0.134    0.393 

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: 676
Number of extensions: 30
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: 481
Length of database: 489
Length adjustment: 34
Effective length of query: 447
Effective length of database: 455
Effective search space:   203385
Effective search space used:   203385
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