GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Dinoroseobacter shibae DFL-12

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

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



>lcl|FitnessBrowser__Dino:3609634 Dshi_3017 aldehyde dehydrogenase
           (RefSeq)
          Length = 780

 Score =  330 bits (847), Expect = 8e-95
 Identities = 191/468 (40%), Positives = 271/468 (57%), Gaps = 20/468 (4%)

Query: 22  GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81
           G+FI   F      KTF T +P+   E+ QV +    DI+ AV AA  A   +W+    Q
Sbjct: 34  GVFIGGTF--QAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRA-QPAWARLGGQ 90

Query: 82  VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140
              +VLY +A L+ +H+   A +E LDNGK +  S+  D+ L   +F   AG    ++  
Sbjct: 91  GWARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDE 150

Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200
           + +          R P+GVCGQI+PWNFPLLM +WK+ P L  G T VLK AE TPL+AL
Sbjct: 151 LPD----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTAL 200

Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260
             A +  EAG PPGVVN+V+G G T GA + SHP + K+AFTGST  GR I +A A +  
Sbjct: 201 LFAEICGEAGVPPGVVNIVTGDGAT-GAALVSHPGVDKIAFTGSTDVGREIRRATAGTG- 258

Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320
           K +TLELGGKSP +VF+DAD+ S ++ LV  I++N G+VCCAGSR+ VQEGI +   ++ 
Sbjct: 259 KALTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKL 318

Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIK 380
           +    +L+IGDP  +   +GA        K+ + +     E    +        +G F  
Sbjct: 319 RARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNGE----VHQPGTVPAEGAFYP 374

Query: 381 PTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISV 440
           PT+   ++    ++RDEIFGPV+  T F+T  E + +AN + YGLAA + + N++ A+ +
Sbjct: 375 PTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDI 434

Query: 441 SNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKA 488
           + K+ +G +WVN  N F     FGG  +SG GRE G E L  YT+  A
Sbjct: 435 APKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTKQAA 482



 Score = 88.6 bits (218), Expect = 7e-22
 Identities = 66/216 (30%), Positives = 104/216 (48%), Gaps = 5/216 (2%)

Query: 54  EAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSL 113
           E   +DI +AVEAAT A  +SW  +   +R ++LY +A+ +    +  A   A   G  +
Sbjct: 540 EGSRKDIRNAVEAATGA--ASWGRTTGHLRAQILYYVAENLSARTEEFATRIAEMTGSRV 597

Query: 114 MCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMA 173
             ++ +V+       + A W DK  G+V             EP+GV G   P + PLL A
Sbjct: 598 PRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGA 657

Query: 174 SWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSH 233
              LG  L  G   VL  +E  PL+A  L  ++  +  P GVVN+V+G       P++SH
Sbjct: 658 VSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASH 717

Query: 234 PKIKKV-AFTGSTATGRHIMKAAAESNLKKVTLELG 268
             +  V +F+G+  +    ++A A  NLK+  +  G
Sbjct: 718 LGVDAVWSFSGADIS--TTIEAEAAGNLKRTWVNHG 751


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: 885
Number of extensions: 43
Number of successful extensions: 9
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: 780
Length adjustment: 37
Effective length of query: 458
Effective length of database: 743
Effective search space:   340294
Effective search space used:   340294
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: 53 (25.0 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, 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