GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Desulfobacter vibrioformis DSM 8776

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  314 bits (805), Expect = 4e-90
 Identities = 174/466 (37%), Positives = 268/466 (57%), Gaps = 4/466 (0%)

Query: 7   INGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65
           I  + +  + +K   V NPATG+VL  +    A++   A+ AA+ +   W   T   R+ 
Sbjct: 16  IQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPAWRSKTAAQRSA 75

Query: 66  CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125
            L +  D++ EN +  A L +   GKPL  +   EI      F +FA  A+ + G    +
Sbjct: 76  ILRRWHDLLMENQEDLALLMTAEQGKPLAES-RGEIAYAASFFEWFAEEAKRIYGDIIPQ 134

Query: 126 YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185
            +     ++ + P+GVVA+I PWN+P  M   K   ALAAG  +V+KP+  TP +AL +A
Sbjct: 135 TIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALAIA 194

Query: 186 ELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244
           +LA++   P GV N++ G    +G  LT +P VR ++ TGS   G+ ++   A ++KR  
Sbjct: 195 KLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCAGTMKRVS 254

Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304
           MELGG AP IVFDDAD++A VEG  +  Y N+GQ C  A R+Y Q G+YD   EKL  AV
Sbjct: 255 MELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLARAV 314

Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364
           ATLK G   +E    GPL  +  +E V + + +A   G  KV+ GG++    G +++PT+
Sbjct: 315 ATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKG-AKVLAGGKRHALGGTFFSPTV 373

Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424
           LA    D  + ++E+FGP   +  F++E +VV  AND++YGLA+  +T+D+ R  RV  +
Sbjct: 374 LADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWRVGEK 433

Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470
           L+YG   +N+  +  +  P GG K SG G++ S YGL+DY  ++++
Sbjct: 434 LEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYM 479


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: 514
Number of extensions: 14
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: 485
Length adjustment: 34
Effective length of query: 440
Effective length of database: 451
Effective search space:   198440
Effective search space used:   198440
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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