GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Desulfobacter vibrioformis DSM 8776

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  313 bits (803), Expect = 7e-90
 Identities = 184/470 (39%), Positives = 264/470 (56%), Gaps = 8/470 (1%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI  ++ +A S +     +P  G  L  V  C   +  RA++ A  +  +  W     A+
Sbjct: 15  FIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA--WRSKTAAQ 72

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R A L R+ DLL +N E+LALL T + GKP+ +S   +I  AA    W AE   ++Y ++
Sbjct: 73  RSAILRRWHDLLMENQEDLALLMTAEQGKPLAESRG-EIAYAASFFEWFAEEAKRIYGDI 131

Query: 143 AP-TPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAI 201
            P T   Q  +V ++PVGVV AI PWNFP  M   K G ALA G ++V+KP+  +P +A+
Sbjct: 132 IPQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSAL 191

Query: 202 RIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNM 261
            IA+LA EAG+P GV NV+ G    +G  L  +  V  L FTGST++ K+LM       M
Sbjct: 192 AIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCA-GTM 250

Query: 262 KRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPM 321
           KR+ +E GG +P IVF DA DL AA E A S    N G+ C   +RL V+  + D+F   
Sbjct: 251 KRVSMELGGNAPFIVFDDA-DLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEK 309

Query: 322 VVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGT 381
           +  A+   K GN ++     G L+D + + +V  +I      GAK+LAGGKR     GGT
Sbjct: 310 LARAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR--HALGGT 367

Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441
           +  PT+   VT+ M +A+EEIFGP   +  F++  E V  ANDT YGLAA  +T D+++ 
Sbjct: 368 FFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMART 427

Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            +    +  G + +N     +  APFGG K+SGNGR+ S + L+ Y E+K
Sbjct: 428 WRVGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIK 477


Lambda     K      H
   0.316    0.132    0.390 

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: 572
Number of extensions: 22
Number of successful extensions: 6
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: 497
Length of database: 485
Length adjustment: 34
Effective length of query: 463
Effective length of database: 451
Effective search space:   208813
Effective search space used:   208813
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: 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