GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Phaeobacter inhibens BS107

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__Phaeo:GFF3227 PGA1_c32800 aldehyde
           dehydrogenase
          Length = 802

 Score =  327 bits (838), Expect = 1e-93
 Identities = 191/470 (40%), Positives = 272/470 (57%), Gaps = 25/470 (5%)

Query: 22  GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81
           G FIN EF        F + +P+T E +  + +A   D+D AV+AA  A  + WS +   
Sbjct: 58  GHFINGEFTAPGDG--FDSKNPATGEVLATLSQATQSDVDSAVDAARKA-QTKWSAAGGA 114

Query: 82  VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140
            R + LY +A L+ +HA   A +E LDNGK +  S+  DV L   +F   AG    ++  
Sbjct: 115 ARARYLYAIARLMQKHARLFAVLETLDNGKPIRESRDIDVPLAQRHFYYHAGMAQLMESE 174

Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200
           + +          RE +GVCGQIIPWNFPLLM +WK+ P +  G T VLK AE T L+AL
Sbjct: 175 LPD----------REALGVCGQIIPWNFPLLMLAWKVAPAIAMGNTVVLKPAEYTSLTAL 224

Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260
             A + ++AG P GVVN+V+G G      + +   + K+AFTGSTA GR I +A A S  
Sbjct: 225 LFADICRQAGLPKGVVNIVTGDGAVGEMIVGAD--VDKIAFTGSTAVGRRIREATAGSG- 281

Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320
           K +TLELGGKSP IVFDDAD+ S I+ LV  I++N G+VCCAGSR+ VQEGI ++  ++ 
Sbjct: 282 KALTLELGGKSPYIVFDDADIDSAIEGLVDAIWFNQGQVCCAGSRLLVQEGIAERFHTKL 341

Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYI---DIGKKEGATVITGGERFGNKGY 377
           +   + L+IG+P  +   +GA    +QL  I + +     G+   A V         +G 
Sbjct: 342 RVRMDKLRIGNPLDKSIDVGAIVDPVQLTTISEMVAANTAGRMHQAQVAVP-----ERGC 396

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           F  PT+   +     ++++EIFGPV+  T F+T  E + LAN++ YGLAA + T N++ A
Sbjct: 397 FYPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVELANNTRYGLAATLWTENVNLA 456

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487
           + ++ K+ +G +WVN  N F     FGG  +SG GRE G E L  YT+ K
Sbjct: 457 LDIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGGWEGLSAYTKPK 506



 Score = 77.0 bits (188), Expect = 2e-18
 Identities = 55/212 (25%), Positives = 100/212 (47%), Gaps = 7/212 (3%)

Query: 58  EDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSK 117
           +D+ +AVEAA  A  ++WS +   +R ++LY + + +       A       GKS    +
Sbjct: 568 KDVRNAVEAAAGA--NAWSKTTGHLRAQILYYIGENLSARVGEFADRIDRMTGKSQGAQE 625

Query: 118 GDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKL 177
            + ++   +  + A W DK  G              +EP+GV G +     PLL     +
Sbjct: 626 VEASIQRLF--TAAAWADKYDGQAHGVPIRGVALAMKEPVGVIGALCADEAPLLGLVSVM 683

Query: 178 GPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIK 237
            P +  G   VL  +E+ PLSA     +++ +  P GVVN+++G      +P++SH  + 
Sbjct: 684 APAIAMGNRVVLAASEAYPLSATDFYQVLETSDLPGGVVNILTGRHAEMASPLASHLNVD 743

Query: 238 KV-AFTGSTATGRHIMKAAAESNLKKVTLELG 268
            V +F+ S  +   +++ A+  NLK+  +  G
Sbjct: 744 AVWSFSSSDLSA--MIEEASAGNLKRTWVNNG 773


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: 891
Number of extensions: 43
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 495
Length of database: 802
Length adjustment: 38
Effective length of query: 457
Effective length of database: 764
Effective search space:   349148
Effective search space used:   349148
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, the preprint 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