GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Novosphingobium barchaimii LL02

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_059151695.1 V474_RS11820 succinylglutamate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>NCBI__GCF_001046635.1:WP_059151695.1
          Length = 474

 Score =  456 bits (1172), Expect = e-132
 Identities = 230/453 (50%), Positives = 309/453 (68%), Gaps = 4/453 (0%)

Query: 21  NPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLESNKAELT 80
           +P +GE +W+G  A    V  A   AR AFP WA L  AER A  +R+ A LE+ K  + 
Sbjct: 8   DPATGETVWEGEIAGPQAVSAALLRARKAFPAWAALPVAERVAAAQRYKAALEARKDAIA 67

Query: 81  AIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHRPHGVLAV 140
            IIARETGKP WE  TEV +MI K+ +SI A   R G+++S MP G A LRHRPHGV+AV
Sbjct: 68  QIIARETGKPMWETRTEVASMIGKVGLSITAQAERAGDRQSAMPFGQAVLRHRPHGVMAV 127

Query: 141 FGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQA-GLPPGVLNLVQG 199
            GP+NFPGHLPNGHIVPAL+AGNT++FKPSE+TP +G A+   W +A      V   +QG
Sbjct: 128 LGPFNFPGHLPNGHIVPALIAGNTVVFKPSEMTPATGAAMAECWAEALADHRHVFQCIQG 187

Query: 200 GRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLIIDEVADID 259
            RETG+AL A   +DGLLFTGSA  G    R  + +P+ ILALE+GGNNPLI  + AD+D
Sbjct: 188 ARETGEALVA-GHIDGLLFTGSAGAGAHFRRIFADRPDVILALELGGNNPLIAWDSADVD 246

Query: 260 AAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDEPQPFIG 319
            A  + +QS F+T GQRC+CARRL++   A G A +  +  ++ R+  G W++ P+P+IG
Sbjct: 247 EAASVVVQSGFITTGQRCSCARRLIVPDNAFGAALVDAVAGLADRIVIGAWNETPEPWIG 306

Query: 320 GLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGT-SLLTPGIIEMTGVAGVPDEEVFG 378
            LIS+ AAQ     + +L   G + +     ++  + + +TP I+++TG+  VPDEE+F 
Sbjct: 307 PLISDAAAQAAKARFAELVERGAKVIRPLNGVEGRSGAFVTPAILDVTGIF-VPDEEIFA 365

Query: 379 PLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPLTGAAS 438
           P+L++ R   FD AI  ANNTRFGLS GL+S +   + ++L+E RAG+VN N+P TGAA 
Sbjct: 366 PVLQISRVPDFDAAIEAANNTRFGLSAGLISADDALWQRVLVEGRAGVVNRNRPTTGAAG 425

Query: 439 TAPFGGIGASGNHRPSAWYAADYCAWPMASLES 471
           + PFGG+G SGNHRPSA+YAADYCA+P+AS E+
Sbjct: 426 SMPFGGLGESGNHRPSAYYAADYCAYPVASFEA 458


Lambda     K      H
   0.318    0.134    0.412 

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: 774
Number of extensions: 41
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: 492
Length of database: 474
Length adjustment: 34
Effective length of query: 458
Effective length of database: 440
Effective search space:   201520
Effective search space used:   201520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 24 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