GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Herbaspirillum seropedicae SmR1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__HerbieS:HSERO_RS05115
          Length = 793

 Score =  353 bits (906), Expect = e-101
 Identities = 197/446 (44%), Positives = 268/446 (60%), Gaps = 15/446 (3%)

Query: 57  VNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDR 116
           ++P++G+++  +++G   DVD AV+AA+AA      W+ +    R R L  LA  ++R  
Sbjct: 51  IDPASGKLLAHLSQGSAADVDAAVQAAQAALP---GWQALGGHGRARHLYALARTVQRHA 107

Query: 117 TYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPV 176
             LA LETLDNGKP   S  VD+ +V +   +YAGWA     +          +  H PV
Sbjct: 108 RLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQESE----------FPDHVPV 157

Query: 177 GVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVN 236
           GV GQI+PWNFPLLM AWK+ PALA GN VV+K AE T LTAL  A L ++AG P GV+N
Sbjct: 158 GVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSLTALLFAELAQQAGLPAGVLN 217

Query: 237 IVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGKSPNIIMS 296
           IV G G T GAA+ +H  + K+AFTGSTE+GR+I+     S  K +TLELGGKSP I+  
Sbjct: 218 IVTGDGAT-GAAVVAHPGIQKIAFTGSTEVGRLIREQTAGSG-KSLTLELGGKSPFIVFE 275

Query: 297 DADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKT 356
           DAD+D A+E    A++FNQGQ CCAGSR  VQE I+D F+ R   R +   VG P D  +
Sbjct: 276 DADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHDLFIARLKTRMQKLKVGAPLDKCS 335

Query: 357 EQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEE 416
           + G  +   Q +++   +  G +EGA+           G F  PT+   V    T+A EE
Sbjct: 336 DMGALISPVQLERVRSLVEQGVREGAQCHQVVLDTPPGGCFYPPTLLTGVHPAATVASEE 395

Query: 417 IFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVF 476
           IFGPV+  + F+T +E V  ANNS YGLAA+++++ +  A  ++  L+AG VW+N  + F
Sbjct: 396 IFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETIGLALGVAPQLKAGVVWINSTNQF 455

Query: 477 GAQSPFGGYKMSGSGRELGEYGLQAY 502
            A   FGG + SG GRE G  G   Y
Sbjct: 456 DAAVGFGGVRESGYGREGGREGCYEY 481



 Score = 75.9 bits (185), Expect = 5e-18
 Identities = 62/226 (27%), Positives = 96/226 (42%), Gaps = 6/226 (2%)

Query: 62  GEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLAA 121
           GE +  V  G+++D+  AV AA  A      W       R + L  +A+ +   RT   A
Sbjct: 542 GERLEDVGLGNRKDIRNAVAAAVKA----GGWTSASPHRRAQGLYYIAENLSA-RTEEFA 596

Query: 122 LETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQ 181
                           ++D  +K L  Y  WADK+ G          +    E +GV G 
Sbjct: 597 RRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALAMPEAIGVVGV 656

Query: 182 IIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGF 241
           + P   PLL     + P +A GN VV+  +EQ PL A  +  ++  +  P GV+NIV G 
Sbjct: 657 VCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLPAGVINIVTGK 716

Query: 242 GPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELG 287
                  +A H++V+ +   G  E     +    + NLKR  ++ G
Sbjct: 717 SAELLPVLAEHDEVEALWVRGPAEFSATAE-RLSTGNLKRCFVDHG 761


Lambda     K      H
   0.319    0.136    0.409 

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: 952
Number of extensions: 51
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: 517
Length of database: 793
Length adjustment: 38
Effective length of query: 479
Effective length of database: 755
Effective search space:   361645
Effective search space used:   361645
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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