GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Desulfobacter vibrioformis DSM 8776

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P49419
         (539 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  205 bits (522), Expect = 3e-57
 Identities = 135/447 (30%), Positives = 212/447 (47%), Gaps = 6/447 (1%)

Query: 71  PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130
           PA  E +  V      +    +  A  +   W    A +R  I+R+  D L E  + L  
Sbjct: 34  PATGEVLGTVPFCGADETRRAIDAANGSLPAWRSKTAAQRSAILRRWHDLLMENQEDLAL 93

Query: 131 LVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVGI 190
           L++ E GK L E  GE+       ++    ++ I G I+P   +   L+    PVG+V  
Sbjct: 94  LMTAEQGKPLAESRGEIAYAASFFEWFAEEAKRIYGDIIPQTIASQRLVVIKQPVGVVAA 153

Query: 191 ITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICSL 250
           IT +NFP A+       A+  G   + K A  T   ++A+ K+     E    PG    +
Sbjct: 154 ITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALAIAKLAQ---EAGMPPGVFNVV 210

Query: 251 TCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNNAIIAFEDAD 310
           T   + IG  +  +  V  L+FTGST+VGK++         R  +ELGGN   I F+DAD
Sbjct: 211 TGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCAGTMKRVSMELGGNAPFIVFDDAD 270

Query: 311 LSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNVLYG 370
           L   V  AL      +GQ C  A RL++   ++D+   +L +A A ++VGN  +  V+ G
Sbjct: 271 LDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLARAVATLKVGNGIEEGVVQG 330

Query: 371 PLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLGHDASIAHTETFA 430
           PL   +AV      + +A  +G  V+ GGK     G +  PT++  +  D  +A  E F 
Sbjct: 331 PLIDMKAVESVERHINDALDKGAKVLAGGKRHALGGTFFSPTVLADVTDDMLVAKEEIFG 390

Query: 431 PILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGA 490
           P   +FKF++E EV    N+ + GL++  FT+D+ R +R +G K  + G++ +N      
Sbjct: 391 PFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWR-VGEK-LEYGLIGINSGIISN 448

Query: 491 EIGGAFGGEKHTGGGRESGSDAWKQYM 517
            +   FGG K +G GRE        Y+
Sbjct: 449 AV-APFGGVKESGNGREGSKYGLDDYL 474


Lambda     K      H
   0.318    0.136    0.417 

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: 674
Number of extensions: 24
Number of successful extensions: 3
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: 539
Length of database: 485
Length adjustment: 35
Effective length of query: 504
Effective length of database: 450
Effective search space:   226800
Effective search space used:   226800
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 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