GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Denitrovibrio acetiphilus DSM 12809

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_013010594.1 DACET_RS06525 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_000025725.1:WP_013010594.1
          Length = 454

 Score =  160 bits (406), Expect = 6e-44
 Identities = 143/475 (30%), Positives = 231/475 (48%), Gaps = 52/475 (10%)

Query: 2   RLFGTAGIRGTLWE-KVTPELAMKVGMAV------GTYKSGKALVGRDGRTSSVMLKNAM 54
           + FGT G+RG   E  +T   A+++G AV      G  K  K ++G+D R S  M ++A+
Sbjct: 3   KYFGTDGVRGKANEFPMTATFALRLGQAVAKQFSNGGKKIHKVVIGKDTRVSGYMFESAL 62

Query: 55  ISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFY 113
           +SG+ S G++ +   ++PTPA+++ TR L ADAGV+I+ASHNP  DNG+K F+GDG +  
Sbjct: 63  VSGITSMGLDAVLVGVLPTPAISFITRSLRADAGVVISASHNPYYDNGIKFFSGDGYKLP 122

Query: 114 VEQERGLEEI-----------IFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN 162
            E E  +E+            I +    KA   +    R VE      +  +D  G    
Sbjct: 123 DETEISIEQTTDEMIQNGEIPISTDRIGKAYRVDTAIGRYVEFSKSTFDKDIDLSG---- 178

Query: 163 LKVLYDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVREL 222
           ++++ D +NGA   VAP    E+ AK+  +    DG          Y   A   K V+E 
Sbjct: 179 MRLVVDCSNGANYKVAPMAFEELAAKINVMGNEPDGMNINSGCGSVYPE-AMCAK-VKEK 236

Query: 223 GVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRI 279
           G DL I+ DGD DR+   DE G  VD D ++ + AK Y+   G     T+V ++ +    
Sbjct: 237 GADLGISFDGDGDRVIFSDENGEMVDGDIIMGICAK-YMNSLGYLNKNTMVCTVMSNFGF 295

Query: 280 DAVVERAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIK 336
           +  +  AG ++VR  +G  +   + +K    +   +   ++   +    D  V+   L+K
Sbjct: 296 EKSMLEAGVKLVRTDVGDRYVMAEMLKNGYNLGGEQSGHIIFSDYNTTGDGLVSAMQLLK 355

Query: 337 LIDENG-PLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISG 395
           +I  +G PLSEL K I  Y     N     +   + + R ++E++  ++ E+        
Sbjct: 356 VIVRSGKPLSELKKFITLYPQVLKNFKVQKKIPVDYLERTSKEIQ-AVNKEL-------- 406

Query: 396 FRIALNDGSW-ILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKEAEK 449
                 DG+  +L+R SGTE K+RV+ E     R   + E A +  +  VKE E+
Sbjct: 407 ------DGTGRVLVRYSGTENKLRVMLEGEDLSR---ITEYAENIGANAVKEIEE 452


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: 516
Number of extensions: 29
Number of successful extensions: 5
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: 454
Length adjustment: 33
Effective length of query: 417
Effective length of database: 421
Effective search space:   175557
Effective search space used:   175557
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