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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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