Alignments for a candidate for adh in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Caulobacter crescentus NA1000

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_01679 CCNA_01679 succinylglutamic semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Caulo:CCNA_01679
          Length = 485

 Score =  471 bits (1213), Expect = e-137
 Identities = 244/471 (51%), Positives = 320/471 (67%), Gaps = 7/471 (1%)

Query: 3   LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62
           L+I+G W  GQGA     +P +GE +W    A  A V  A  AAR AFP WA     ER 
Sbjct: 5   LFIDGKWRAGQGAGLSSTDPATGEDVWSAATATPADVADAVAAARKAFPAWADRPREERI 64

Query: 63  AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122
           A++ R+  +L    A     ++RETGK  WE   E+ +M  K+ +SI+AY  RTG   + 
Sbjct: 65  AILRRYKDILVERAAPYAEALSRETGKALWETRAELASMAGKVDLSIRAYDERTGVTENA 124

Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182
           MP G A LRHR HGV+AV GP+NFPGHLPNGHIVPALLAG+T++FKPSE TP +G+ ++ 
Sbjct: 125 MPFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLMVE 184

Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242
             + AG P GV+NLVQGGRETGQAL A +D+DGLLFTGSA  G    R  + +P+ ILAL
Sbjct: 185 ALEAAGAPAGVVNLVQGGRETGQALIA-QDIDGLLFTGSAAAGTYFRRYFADRPDVILAL 243

Query: 243 EMGGNNPLIIDEVADI-DAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301
           E+GGNNPL++    D  +A   L +QSAF+T GQRC+CARRL++   A G A +   VA+
Sbjct: 244 ELGGNNPLVVWNADDAPEAVAALIVQSAFITTGQRCSCARRLIVPDDASGAAIIEATVAL 303

Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLA-PRLLQAGTSLLTP 360
           ++RL  G W+ E +PF+G LIS +AA+    A +   A  G+ +LA   +   G + L P
Sbjct: 304 AERLVIGAWNAENEPFMGPLISGRAAK---AAREVASATPGKTILALDGVAGLGDAFLKP 360

Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420
           GI+++TG+   PDEE+F PLL+V R  +FDEA+  AN TR+GLS GL+S E E +D+ L 
Sbjct: 361 GIVDVTGLE-TPDEELFAPLLQVRRVSSFDEALAAANATRYGLSAGLISNESELWDKFLS 419

Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLES 471
             RAG+VNWN+P TGAA + PFGG+GASGNHRPSA+YAADYCA+P+AS E+
Sbjct: 420 RIRAGVVNWNRPTTGAAGSMPFGGLGASGNHRPSAYYAADYCAYPVASFEA 470


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: 777
Number of extensions: 29
Number of successful extensions: 5
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: 485
Length adjustment: 34
Effective length of query: 458
Effective length of database: 451
Effective search space:   206558
Effective search space used:   206558
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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources