GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Desulfacinum infernum DSM 9756

Align Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized)
to candidate WP_073040272.1 BUB04_RS13170 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::Q72IB8
         (307 letters)



>NCBI__GCF_900129305.1:WP_073040272.1
          Length = 995

 Score =  121 bits (303), Expect = 8e-32
 Identities = 94/312 (30%), Positives = 144/312 (46%), Gaps = 49/312 (15%)

Query: 34  RYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLEL--VWALAGKP 91
           +++AG    EAL   E +  +G+    DLLGE V + EE  A+    L+L  V   A + 
Sbjct: 117 QFIAGADAREALPVLEKMRAQGLAFTADLLGEAVVSREEEEAYLERYLDLFDVLGTAARS 176

Query: 92  W-----------------------PKYISLKLTQLGLDLSEDLALALLREVLREAEPRGV 128
           W                       P  +  ++     D S D A   LR + R+A   G 
Sbjct: 177 WKALGDGAGDLDWGWAPKLNVSIKPSAMYSQMNACAFDYSVDRAKDRLRPLFRKAMELGA 236

Query: 129 FVRLDMEDSPRVEATLRLYRALREE----GFSQVGIVLQSYLYRTEKDLLDLLPY-RPN- 182
           FV LDME +     TL LY++L EE    G+   G+V+Q+YL  +E DL DL+ + R N 
Sbjct: 237 FVCLDMEHTALKNITLALYKSLMEEPEFRGYPHTGVVIQAYLRDSEADLRDLIDWARKNR 296

Query: 183 ----LRLVKGAYREPKEV----------AFPDKRLIDAEYLHLGKLALKEGLYVAFA--T 226
               +RLVKGAY + + +           + +K   DA +  L +L ++   +V FA  +
Sbjct: 297 QPCTVRLVKGAYWDAEVIWARQNHWPVPVYTNKYDTDANFEKLARLLMENSAHVGFACAS 356

Query: 227 HDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGR--DWYP 284
           H+ R +A +   ++ + +P  R E+Q LYG+    +  L + G  +R Y P G       
Sbjct: 357 HNIRSLAYVIELSKDLKVPEDRIEYQILYGMAEPVRTALKKAGLPLRLYTPIGEMIPGMA 416

Query: 285 YLTRRIAERPEN 296
           YL RR+ E   N
Sbjct: 417 YLVRRLLENTSN 428


Lambda     K      H
   0.323    0.141    0.407 

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: 623
Number of extensions: 34
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: 307
Length of database: 995
Length adjustment: 35
Effective length of query: 272
Effective length of database: 960
Effective search space:   261120
Effective search space used:   261120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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