GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS05115
          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:

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