GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Herbaspirillum seropedicae SmR1

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS04810 HSERO_RS04810 aldehyde
           dehydrogenase
          Length = 504

 Score =  316 bits (809), Expect = 1e-90
 Identities = 176/469 (37%), Positives = 254/469 (54%), Gaps = 6/469 (1%)

Query: 7   INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66
           INGELV+G+GE   +YNPATG   L   +  A  V+AA  AA  A  +W   +   R   
Sbjct: 27  INGELVAGQGEIIQLYNPATGRASLSYRDGGAAAVEAAAVAAQRAQRQWWALSHAARGRA 86

Query: 67  LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126
           L  +  VI    +  A LE+ + GKP+      E+  + ++F ++AG A    G      
Sbjct: 87  LYAVGAVIRAEAEPLARLEAISSGKPIRDC-RAEMQKVAEMFEYYAGWADKFYGEVI-PV 144

Query: 127 LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE 186
              H +  RR+P G V  + PWN P     W+L PALA GN V+LKPSE+TP ++L +A 
Sbjct: 145 PSSHLNYTRREPYGTVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPFSSLAIAR 204

Query: 187 LAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHM 245
           L +    PAG++N+L G G+T+         V+ V   GS ATG  I    A+ +    +
Sbjct: 205 LGEQAGLPAGLVNVLAGLGQTMVPQAMATWTVKKVIFVGSPATGALIAKAAAARVMPCVL 264

Query: 246 ELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVA 305
           ELGGK+  I+F+DAD+     G +   +  AGQ C A  R+  Q+ +YD  VE + A   
Sbjct: 265 ELGGKSANIIFEDADLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRFVETVAAGAE 324

Query: 306 TLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGN-GYYYAPTL 364
            ++ GAP D+STE+GP+++    E + + V      G    +  G  R G  GY+  PTL
Sbjct: 325 KIRLGAPLDDSTEVGPINNRKQYEHIQRMVARGLEAG--ATLAAGHTRYGEEGYFVRPTL 382

Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424
           LA A     + + E+FGPV    PF++EE+ +  ANDS++GLA +VWT+DV RAHRV+A 
Sbjct: 383 LAHASNAMEVARSEIFGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDVARAHRVAAS 442

Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
           +  G  WVN++  +    P GG   SGYG+   +  L DYT  + V V+
Sbjct: 443 VNAGTFWVNSYKTINVASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491


Lambda     K      H
   0.317    0.134    0.397 

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: 632
Number of extensions: 26
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 474
Length of database: 504
Length adjustment: 34
Effective length of query: 440
Effective length of database: 470
Effective search space:   206800
Effective search space used:   206800
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: 52 (24.6 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