GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_068170492.1 HTA01S_RS10485 aldehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_001592305.1:WP_068170492.1
          Length = 492

 Score =  195 bits (495), Expect = 3e-54
 Identities = 152/459 (33%), Positives = 226/459 (49%), Gaps = 13/459 (2%)

Query: 12  AGQGETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFP--AWARRPLEQRIELLER 68
           A  G+T + + PV G+ +    RG  A  +DAAV A R AF    W+     QR  ++ +
Sbjct: 22  ARDGQTFDCISPVDGRVLTQVARGGQA-DIDAAVAAGRAAFEDRRWSGMAPAQRKRVMIK 80

Query: 69  FAATLKSRADELARVIGEETGKPL-WESATEVTSMVNKVAISVQAFRERTGEKSGPLADA 127
           FA  L + ADELA     + GKP+ +  A +V S  N +    +A  +   E +   A+A
Sbjct: 81  FADQLLAHADELALTETLDMGKPVKYARAVDVNSAANCIRWYGEAVDKVYDEIAPTGANA 140

Query: 128 TAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQ 187
            A++  +P GVV +  P+N+P  +    I PAL AGN VV KPSE +P  A    +  + 
Sbjct: 141 LALITREPVGVVGIIVPWNYPMIMAAWKIAPALAAGNSVVLKPSEKSPLTALRLAELALA 200

Query: 188 AGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMG 246
           AG+P GV N+V G G E G  LA H  +D + FTGS+R G  +H   G    K    E+G
Sbjct: 201 AGIPPGVFNVVPGFGTEAGSPLALHMDVDCIAFTGSTRVGKQIHVMAGQSNLKRAWTELG 260

Query: 247 GNNP-LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSAT 305
           G +P +V  +  DLD AV   + S F + G+ C    RL V + +  DA L + + +   
Sbjct: 261 GKSPNIVFADCPDLDRAVEAAVGSIFFNQGESCNAPSRLFV-EASIKDAFLEKALKLVPQ 319

Query: 306 LRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLL--AMTQPIDGAALLTPGI 363
            + G         MGA++     +++++       +GAQ +   A+  P+ G   + P I
Sbjct: 320 YQPGN-PLDKGTVMGAIVDQMQLDNVMRYIGLGQSEGAQLIAGGALASPVAGGCYVQPTI 378

Query: 364 LD-VSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVE 422
            D V+       EE FGP+L V  ++D A  +R AN + YGL AG+ +    +       
Sbjct: 379 FDGVTPQMTIAREEIFGPVLAVQSFTDAADVVRAANNSVYGLQAGVWTRDINKAHGVARA 438

Query: 423 SRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461
            RAG V+ N Q      + PFGG   SG  R  + +A D
Sbjct: 439 LRAGTVHVN-QYDEDDITVPFGGFKQSGVGRDKSLHAFD 476


Lambda     K      H
   0.318    0.134    0.396 

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: 575
Number of extensions: 26
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: 487
Length of database: 492
Length adjustment: 34
Effective length of query: 453
Effective length of database: 458
Effective search space:   207474
Effective search space used:   207474
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