GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB in Pseudomonas putida KT2440

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate PP_4716 PP_4716 Phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>lcl|FitnessBrowser__Putida:PP_4716 PP_4716 Phosphoglucosamine
           mutase
          Length = 446

 Score =  144 bits (362), Expect = 7e-39
 Identities = 131/445 (29%), Positives = 209/445 (46%), Gaps = 37/445 (8%)

Query: 2   RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTY--KSG--KALVGRDGRTSSVMLKNAMIS 56
           + FGT GIRG + E  +TP+  +K+G A G    K G  + LVG+D R S  M ++A+ +
Sbjct: 4   KYFGTDGIRGRVGEYPITPDFMLKLGWAAGMAFRKQGHCRVLVGKDTRISGYMFESALEA 63

Query: 57  GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115
           GL + G +V+    +PTPA+A+ TR   A+AG++I+ASHNP  DNG+K F+G GT+   E
Sbjct: 64  GLSAAGADVMLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGQGTKLPDE 123

Query: 116 QERGLEE-------IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168
            E  +EE       ++ SG   K         R +E     + +   F G    LK++ D
Sbjct: 124 VELMIEELLDQPMTVVESGKLGKVSRINDAAGRYIEFCKSSVPSSTSFEG----LKLVVD 179

Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228
            A+GA   VAP + RE+GA V  ++A  DG          +        LV     DL I
Sbjct: 180 CAHGATYKVAPSVFRELGADVTVLHAQPDGLNINEGCGSTHIESLQAAVLVGH--ADLGI 237

Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG--GGTVVVSIDTGSRIDAVVERA 286
           A DGD DR+ + D  G  VD D ++ + A+  ++EHG   G VV ++ +   ++  ++  
Sbjct: 238 AFDGDGDRVLMVDHTGAIVDGDELLFIIAR-DLQEHGKLQGGVVGTLMSNLGLELALKDL 296

Query: 287 GGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDENGP 343
               VR  +G  +   + ++R   +       +V        D  +    ++  +   G 
Sbjct: 297 DIPFVRAKVGDRYVMAELLEREWLVGGENSGHVVCCNHTTTGDAIIAALQVLMALKRRG- 355

Query: 344 LSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDG 403
             E + +      K   VL    + A  V        ++ S+++ E L   G        
Sbjct: 356 --ETLAQARQALRKCPQVLINVRFGASKVDPLEHPAVKEASAKVTEALAGRG-------- 405

Query: 404 SWILIRPSGTEPKIRVVAEAPTEKR 428
             +L+R SGTEP +RV+ E   E +
Sbjct: 406 -RVLLRKSGTEPLVRVMVEGEDESQ 429


Lambda     K      H
   0.318    0.138    0.402 

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: 444
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 450
Length of database: 446
Length adjustment: 33
Effective length of query: 417
Effective length of database: 413
Effective search space:   172221
Effective search space used:   172221
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. 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 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