GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Caulobacter crescentus NA1000

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03243 CCNA_03243 NADP+-dependent
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          Length = 499

 Score =  360 bits (924), Expect = e-104
 Identities = 192/479 (40%), Positives = 286/479 (59%), Gaps = 5/479 (1%)

Query: 20  PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTS 78
           P+   I+ + V++ S  TF  VSP   + +  V    ++D++ AV  A AAF    W   
Sbjct: 20  PSQAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQ 79

Query: 79  DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKI 137
            P+ +  VL++LA+L++  AD LA +E+LD GK +  ++  D+ L     R  A   DK+
Sbjct: 80  GPRQKKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKV 139

Query: 138 KGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197
            G V  +     +Y   EP+GV G I+PWNFPL MA WK+ P L  G + VLK AE +PL
Sbjct: 140 YGEVGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPL 199

Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257
           +AL L +L  EAG PPGV+NV+ G G  AG  ++    +  +AFTGS   GR +M+ +A 
Sbjct: 200 TALKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSAR 259

Query: 258 SNLKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           SNLK+V+LELGGKSP IVF D  D+++  Q    G+FYN GEVC A SR+ V+  I D  
Sbjct: 260 SNLKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAF 319

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK- 375
           ++     A+ +K+GDP    T  GA  S+ Q++  L YI     +GA  + GG+R   + 
Sbjct: 320 LARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQEA 379

Query: 376 -GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434
            G++++PTIF  V+ D  + R+E+FGPV+ +  F + +E + LAND+ YGLAAG+ T ++
Sbjct: 380 GGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADV 439

Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
           S A+  + ++ +G +WVN ++     +PFGG+ QSG GR+    AL  Y  +K+V + L
Sbjct: 440 SKALRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLKSVSVTL 498


Lambda     K      H
   0.316    0.133    0.389 

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: 551
Number of extensions: 26
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: 495
Length of database: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
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 (21.6 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 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