GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-15108
         (486 letters)



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

 Score =  337 bits (863), Expect = 1e-96
 Identities = 193/465 (41%), Positives = 268/465 (57%), Gaps = 21/465 (4%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73
           FI G F     GKTF   NPA   +L  V +G  A+I+ AV AA++A    W ++     
Sbjct: 36  FIGGTF--QAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRA-QPAWARLGGQGW 92

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133
             VL  +  L+ +     +VLE+LD GKP   S  IDIP A  +F++ +     + +E  
Sbjct: 93  ARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDELP 152

Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193
                      R PVGV G I PWN PLL++ WK+APALA GNTVV+KPAE TP+TA + 
Sbjct: 153 D----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLF 202

Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253
           AEIC +AGVP GVVN+V G G  + GAAL  HP V+ I+FTG T  G+ I  + A T K 
Sbjct: 203 AEICGEAGVPPGVVNIVTGDG--ATGAALVSHPGVDKIAFTGSTDVGREIRRATAGTGKA 260

Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313
           L+ ELGGK+P V+F D++LD  +E  + + + NQG+VC  GSR+ V+    EAF  K  A
Sbjct: 261 LTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKLRA 320

Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLE 373
           +   L +GDP D    VGA++   H  +V    ++     G +   G  P    +G F  
Sbjct: 321 RMATLRIGDPLDKCIDVGAMVDPAHCAKVA---EMVAGSNGEVHQPGTVP---AEGAFYP 374

Query: 374 PTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRV 433
           PT+ITGL     ++++EIFGPV+    F T  E +E  N T YGL+A++W+ ++ RA  +
Sbjct: 375 PTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDI 434

Query: 434 AGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478
           A ++ AG+VWVN   L D    FGG+++SG GREGG      Y++
Sbjct: 435 APKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTK 479



 Score = 78.2 bits (191), Expect = 1e-18
 Identities = 74/223 (33%), Positives = 100/223 (44%), Gaps = 20/223 (8%)

Query: 39  LGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLD 98
           LG   EG   +I  AV+AA  A +  W + T + R  +L  V + +  R EE +   +  
Sbjct: 535 LGHAPEGSRKDIRNAVEAATGAAS--WGRTTGHLRAQILYYVAENLSARTEEFATRIAEM 592

Query: 99  TGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIR-------RPVGVI 151
           TG          +PRA        D + T    A + D       IR        PVGVI
Sbjct: 593 TGSR--------VPRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVI 644

Query: 152 GLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNLVH 211
           G   P + PLL     L  ALA GN +V+ P+E  P+ AT L ++   + VP GVVN+V 
Sbjct: 645 GAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVT 704

Query: 212 GFGPNSAGAALTEHPDVNAI-SFTGETTTGKIIMASAAKTLKR 253
           G    +    L  H  V+A+ SF+G       I A AA  LKR
Sbjct: 705 G-AHEALAKPLASHLGVDAVWSFSG-ADISTTIEAEAAGNLKR 745


Lambda     K      H
   0.318    0.136    0.404 

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: 910
Number of extensions: 35
Number of successful extensions: 6
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: 486
Length of database: 780
Length adjustment: 37
Effective length of query: 449
Effective length of database: 743
Effective search space:   333607
Effective search space used:   333607
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 (21.7 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