GapMind for catabolism of small carbon sources

 

Alignments 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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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