GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Escherichia coli BW25113

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 17247 b3176 phosphoglucosamine mutase (NCBI)

Query= BRENDA::Q6I7B6
         (450 letters)



>FitnessBrowser__Keio:17247
          Length = 445

 Score =  140 bits (354), Expect = 6e-38
 Identities = 131/455 (28%), Positives = 210/455 (46%), Gaps = 51/455 (11%)

Query: 2   RLFGTAGIRGTLWEK-VTPELAMKVGMAVGT----YKSGKALVGRDGRTSSVMLKNAMIS 56
           + FGT GIRG + +  +TP+  +K+G A G     + S K ++G+D R S  ML++A+ +
Sbjct: 5   KYFGTDGIRGRVGDAPITPDFVLKLGWAAGKVLARHGSRKIIIGKDTRISGYMLESALEA 64

Query: 57  GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115
           GL + G+  L    +PTPA+A+ TR   A+AG++I+ASHNP  DNG+K F+ DGT+    
Sbjct: 65  GLAAAGLSALFTGPMPTPAVAYLTRTFRAEAGIVISASHNPFYDNGIKFFSIDGTKLPDA 124

Query: 116 QERGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHE---TNLKVLYDGANG 172
            E  +E  +          +  K  R V+    YI        +E   + LK++ D ANG
Sbjct: 125 VEEAIEAEMEKEISCVDSAELGKASRIVDAAGRYIEFCKATFPNELSLSELKIVVDCANG 184

Query: 173 AGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIAQDG 232
           A   +AP +LRE+GA V+++    +G       E    ++  L   V     DL IA DG
Sbjct: 185 ATYHIAPNVLRELGANVIAIGCEPNG--VNINAEVGATDVRALQARVLAEKADLGIAFDG 242

Query: 233 DADRIAVFDEKGNYVDEDTVIALFAKLYVEE---HGGGTVVVSIDTGSRIDAVVERAGGR 289
           D DR+ + D +GN VD D ++ + A+  + +    GG    +  + G  ++  +++ G  
Sbjct: 243 DGDRVIMVDHEGNKVDGDQIMYIIAREGLRQGQLRGGAVGTLMSNMG--LELALKQLG-- 298

Query: 290 VVRIPLGQPHDGIKRYKAIFAAEPWKLVHPKFGPWI--DPFVT-------MGLLIKLIDE 340
              IP  +   G +        + W++     G  I  D   T       + +L  +   
Sbjct: 299 ---IPFARAKVGDRYVLEKMQEKGWRIGAENSGHVILLDKTTTGDGIVAGLQVLAAMARN 355

Query: 341 NGPLSELVKEIPTYYLKKANVL----CPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGF 396
           +  L +L   +  +     NV       D  + E V+    EVE                
Sbjct: 356 HMSLHDLCSGMKMFPQILVNVRYTAGSGDPLEHESVKAVTAEVE---------------- 399

Query: 397 RIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDE 431
             AL +   +L+R SGTEP IRV+ E   E +  E
Sbjct: 400 -AALGNRGRVLLRKSGTEPLIRVMVEGEDEAQVTE 433


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: 456
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