GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Herbaspirillum seropedicae SmR1

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS05115 HSERO_RS05115 aldehyde
           dehydrogenase
          Length = 793

 Score =  340 bits (873), Expect = 8e-98
 Identities = 192/478 (40%), Positives = 275/478 (57%), Gaps = 16/478 (3%)

Query: 16  TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75
           ++E   G FI   F Q K+      + P++ + +  + +  + D+D AV+AA AA    W
Sbjct: 28  SHEASFGHFIAGRFTQPKAD--LDDIDPASGKLLAHLSQGSAADVDAAVQAAQAAL-PGW 84

Query: 76  STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWT 134
                  R + LY LA  +  HA  LA +E LDNGK L  S+  DV L A +F   AGW 
Sbjct: 85  QALGGHGRARHLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWA 144

Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194
              +            +    P+GV GQI+PWNFPLLM +WK+ P L  G T VLK AE+
Sbjct: 145 QLQESE----------FPDHVPVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAEN 194

Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254
           T L+AL  A L ++AG P GV+N+V+G G T GA + +HP I+K+AFTGST  GR I + 
Sbjct: 195 TSLTALLFAELAQQAGLPAGVLNIVTGDGAT-GAAVVAHPGIQKIAFTGSTEVGRLIREQ 253

Query: 255 AAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314
            A S  K +TLELGGKSP IVF+DAD+ + I+ +V  I++N G+VCCAGSR+ VQEGI+D
Sbjct: 254 TAGSG-KSLTLELGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHD 312

Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN 374
             ++  K   + LK+G P  + + MGA  S +QL+++   ++ G +EGA           
Sbjct: 313 LFIARLKTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVREGAQCHQVVLDTPP 372

Query: 375 KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434
            G F  PT+   V     +  +EIFGPV+    F+T +E + LAN+S YGLAA + +  +
Sbjct: 373 GGCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETI 432

Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492
             A+ V+ ++ +G +W+N+ N F   V FGG  +SG GRE G E    Y + +  + G
Sbjct: 433 GLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGREGGREGCYEYLKPRRQQAG 490



 Score = 69.7 bits (169), Expect = 4e-16
 Identities = 59/247 (23%), Positives = 107/247 (43%), Gaps = 13/247 (5%)

Query: 29  FVQSKSKKTFGTVSPSTE----EEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRM 84
           ++  K  +  G VS +      E +  V     +DI +AV AA  A    W+++ P  R 
Sbjct: 521 YIGGKQVRPDGEVSMACHSTQGERLEDVGLGNRKDIRNAVAAAVKA--GGWTSASPHRRA 578

Query: 85  KVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIET 144
           + LY +A+ +    +  A   A   G +   ++ +V  +     +   W DK +G+V + 
Sbjct: 579 QGLYYIAENLSARTEEFARRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQP 638

Query: 145 GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLAS 204
                     E IGV G + P   PLL     + P++  G   V+  +E  PL A  L  
Sbjct: 639 PMRGVALAMPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQ 698

Query: 205 LIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGS---TATGRHIMKAAAESNLK 261
           ++  +  P GV+N+V+G        ++ H +++ +   G    +AT   +    +  NLK
Sbjct: 699 VLDTSDLPAGVINIVTGKSAELLPVLAEHDEVEALWVRGPAEFSATAERL----STGNLK 754

Query: 262 KVTLELG 268
           +  ++ G
Sbjct: 755 RCFVDHG 761


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: 899
Number of extensions: 38
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: 793
Length adjustment: 38
Effective length of query: 457
Effective length of database: 755
Effective search space:   345035
Effective search space used:   345035
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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