GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Desulfovibrio vulgaris Hildenborough

Align Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= SwissProt::Q72IB8
         (307 letters)



>lcl|MicrobesOnline__882:208845 DVU3319 proline
           dehydrogenase/delta-1-pyrroline-5-carboxylate
           dehydrogenase
          Length = 1006

 Score =  122 bits (307), Expect = 3e-32
 Identities = 104/335 (31%), Positives = 158/335 (47%), Gaps = 51/335 (15%)

Query: 24  IKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLEL 83
           I+   +G+ R+++ G+  +EA+K    L ++G    +DLLGE   +EEE+ A+ +G  E+
Sbjct: 109 IRSNIEGMARQFIIGDNSKEAVKGLAKLRKDGFTFTVDLLGEATVSEEESEAYAQGYHEV 168

Query: 84  VWALA----------------GKPW---PKY-ISLKLTQL-------GLDLSEDLALALL 116
           V A+A                G  W   PK  +S+K + L        ++ S    L+ L
Sbjct: 169 VDAIAREQEKWKALPGNGPVEGFDWGATPKVNVSIKPSALYSQAKPVDVEGSVRGILSRL 228

Query: 117 REVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREE----GFSQVGIVLQSYLYRTEKD 172
             + R+    G F+ +DME     E TL L++ LR +     +  + IVLQ+YL  TEKD
Sbjct: 229 VPIYRKVVAMGGFLCIDMEQLKYKEMTLELFKRLRSDPEFRHYPHLSIVLQAYLRDTEKD 288

Query: 173 LLDLLPYRPN------LRLVKGAYREPKEV----------AFPDKRLIDAEYLHLGKLAL 216
           L DLL +  +      +RLVKGAY + + V           + DK   D  Y  L    L
Sbjct: 289 LDDLLHWARSEKLPIGIRLVKGAYWDYETVIAKQNGWEIPVWTDKPESDIAYEKLAHRIL 348

Query: 217 KEG--LYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRA 274
           +    +Y A A+H+ R IA +     A+ +P  R+EFQ LYG+    ++ L      VR 
Sbjct: 349 ENSDIVYFACASHNVRTIAAVMETALALNVPEHRYEFQVLYGMAEPVRKGLKNVAGRVRL 408

Query: 275 YVPYGR--DWYPYLTRRIAERPENLLLVLRSLVSG 307
           Y PYG       YL RR+ E   N   + +S   G
Sbjct: 409 YCPYGELIPGMAYLVRRLLENTANESFLRQSFAEG 443


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: 635
Number of extensions: 33
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: 1006
Length adjustment: 36
Effective length of query: 271
Effective length of database: 970
Effective search space:   262870
Effective search space used:   262870
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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