GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Methanococcus aeolicus Nankai-3

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011973151.1 MAEO_RS02160 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_000017185.1:WP_011973151.1
          Length = 452

 Score =  275 bits (702), Expect = 3e-78
 Identities = 170/460 (36%), Positives = 260/460 (56%), Gaps = 36/460 (7%)

Query: 1   MRLFGTAGIRGTLWEKVTPELAMKVGMAVGTYKSGKALVGRDGRTSSVMLKNAMISGLLS 60
           M+LFGT+GIR    + +TPE+A KVG AV        +VGRD RT+  +++N++ +GLL+
Sbjct: 1   MKLFGTSGIR---MKNLTPEIAYKVGFAVSQIAKN-VVVGRDTRTTGDLIRNSLFAGLLN 56

Query: 61  TGMEVLDADLIPTPALAWGTRKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGL 120
            G E++D  ++PTP L +  R   D G+MITASHNP   NG+K+FN DGT F  EQE+ +
Sbjct: 57  GGAEIVDIGIVPTPTLGYSARNY-DMGIMITASHNPSEYNGIKLFNKDGTSFRPEQEQNI 115

Query: 121 EEIIFSG-NFRKARWDEIKPVRNVE-VIPDYINAVLDFVGHETNLKVLYDGANGAGSLVA 178
           E+II++  N ++  W+ IK V   E  +  Y + +LD V    N  V+ D AN AG + +
Sbjct: 116 EDIIYNKKNQKRVSWNSIKKVWTDESALKKYSDFILDSVEINKNFSVVVDCANSAGCVAS 175

Query: 179 PYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVD------LAIAQDG 232
           PYL  ++GA V+SVN H+DG F GR PEP  +N+     +++ L  +      + IA DG
Sbjct: 176 PYLFTDVGAHVISVNGHIDGRFIGRSPEPNEKNLQDTMHMIKGLNENNKGNKYIGIAHDG 235

Query: 233 DADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVR 292
           DADR+   DEKG   D D ++A+F++   E+ G  T++ ++D    I+  ++     V+R
Sbjct: 236 DADRMIAIDEKGRLTDFDKLLAVFSRYMAEKTGTKTIITTVDASMAIEEYLKDLNVNVIR 295

Query: 293 IPLGQ--PHDGIKRY-KAIFAAEPWKLVHPKFGPWIDPFVTM---GLL--IKLID----E 340
             +G     D + ++  AIF  EP        G WI   + +   G+L  ++L++     
Sbjct: 296 TKVGDVAVSDELNKHDDAIFGGEP-------SGTWIHKDIHLTPDGILSGLRLLEMMEFY 348

Query: 341 NGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400
           +  L EL+ ++P Y   +  + CPD+ K  V+    +  E    +E++   TI G R +L
Sbjct: 349 DKKLYELIDDVPCYSNLREKLPCPDDKKIIVMDFVIKNGENIFDAEVE---TIDGARFSL 405

Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTV 440
           +DG W+LIRPSGTEP +RV  EA  +    EL E     V
Sbjct: 406 DDG-WVLIRPSGTEPFVRVRVEAKNDIIAKELLEKGIKLV 444


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: 572
Number of extensions: 34
Number of successful extensions: 8
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: 450
Length of database: 452
Length adjustment: 33
Effective length of query: 417
Effective length of database: 419
Effective search space:   174723
Effective search space used:   174723
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 Apr 09 2024. 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