Aligments for a candidate for deoB in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for deoB in Pseudomonas fluorescens FW300-N2E2

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Pf6N2E2_3357 Phosphoglucosamine mutase (EC 5.4.2.10)

Query= BRENDA::Q6I7B6
         (450 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3357
          Length = 445

 Score =  135 bits (339), Expect = 3e-36
 Identities = 128/449 (28%), Positives = 210/449 (46%), Gaps = 50/449 (11%)

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

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

Query: 116 QERGLEE-------IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168
            E  +EE       ++ S    K         R +E     +     F G    LK++ D
Sbjct: 124 IELMIEELLDTPMTVVESSKIGKVSRINDASGRYIEFCKGSVPTGTSFSG----LKIVVD 179

Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228
            A+GA   VAP + RE+GA+V+ ++A  +G          +        L  +   DL I
Sbjct: 180 CAHGATYKVAPSVFRELGAEVVVLSAQPNGLNINHNCGSTHTEALQAAVLAEQ--ADLGI 237

Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGT----VVVSIDTGSRIDAVVE 284
           A DGD DR+ + D  G  VD D ++ + A+   + HG G     VV ++ +   ++  + 
Sbjct: 238 AFDGDGDRVLMVDHTGTVVDGDELLFIIAR---DLHGRGKLQGGVVGTLMSNLGLELALA 294

Query: 285 RAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLV---HPKFGPWIDPFVTMGLLIKLI 338
                 VR  +G  +   + ++R   I       +V   H   G  I   + + + +K  
Sbjct: 295 DLDIPFVRANVGDRYVISELLERNWVIGGENSGHIVCFDHTTTGDAIIAALQVLMALKAR 354

Query: 339 DENGPLS-ELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFR 397
           +E    S + +++ P   +        +  +   V++A+E V + ++   +         
Sbjct: 355 NEGLAQSRQALRKCPQVLINVRFGGGVNPLEHAKVKQASEHVTQAMAGRGR--------- 405

Query: 398 IALNDGSWILIRPSGTEPKIRVVAEAPTE 426
                   +L+R SGTEP +RV+ E   E
Sbjct: 406 --------VLLRKSGTEPLVRVMVEGEDE 426


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: 466
Number of extensions: 27
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: 445
Length adjustment: 33
Effective length of query: 417
Effective length of database: 412
Effective search space:   171804
Effective search space used:   171804
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources