GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Dietzia timorensis ID05-A0528

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_067475179.1 BJL86_RS04440 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>NCBI__GCF_001659785.1:WP_067475179.1
          Length = 455

 Score =  226 bits (575), Expect = 2e-63
 Identities = 159/464 (34%), Positives = 232/464 (50%), Gaps = 38/464 (8%)

Query: 1   MGKLFGTFGVRGIANEEITPEFALKIGMAFGTLL-----------KREGRERPLVVVGRD 49
           M ++FGT GVRG+AN+ +T + AL +G A  ++L               R+RPL V+GRD
Sbjct: 1   MPRMFGTDGVRGLANKSLTVDLALSLGAAAASVLAFDPAADTGHESSRDRQRPLAVIGRD 60

Query: 50  TRVSGEMLKDALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNG 109
            RVSGEML+ AL +GL S G DV+ VG  PTPA+   T H  A  GA+I+ASHNP   NG
Sbjct: 61  PRVSGEMLESALAAGLASQGVDVMLVGQVPTPAVAHLTGHHQAALGAMISASHNPMPDNG 120

Query: 110 IKLLEPNGMGLKKEREAIVEELFFSEDFHRA--KWNEIGELRKEDIIKPYIEAIKNRVDV 167
           IK     G  L  E E  +E+   +        +   I  L +E  + PY+E +   V  
Sbjct: 121 IKFFAAGGRKLSDELEDRIEDALEARITGPTGNRVGRISRLDRETALAPYLEHLLGTV-- 178

Query: 168 EAIKKRRPF----VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEEN 223
                R P     VVVD ++GA     P    + G +VV++NA PDG+    N      +
Sbjct: 179 -----RHPLAGLKVVVDCAHGAAFEAAPAAYAKAGAEVVAINAEPDGY--NINEGVGSTH 231

Query: 224 LKGFMEIVKALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLR--ENGGGLL 281
           ++G    V   GA  G+A DGDADR + +D +G  + GD+  A++A  +    E     L
Sbjct: 232 IEGLQRAVVEHGAALGLAHDGDADRCLAVDASGALVGGDEIMAVLALGMSEAGELKDNTL 291

Query: 282 VTTIATSNLLDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRD 341
           V T+ ++  L      +G  V+ TKVGD  V   L +   ++GGE++G ++ P+     D
Sbjct: 292 VATVMSNLGLHLGLTEHGISVVTTKVGDRYVLEKLADGEYSLGGEQSGHLVLPEHATTGD 351

Query: 342 GAMTTAKIVEIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVA-KVAELAEKKGYK 400
           G +T   ++   A++GK  +EL   +    Q      V    K  V+  V    EK+   
Sbjct: 352 GTLTGLFLMARMAETGKSLAELAAVMTVMPQVLINVQVADKAKVSVSDSVKSAVEKEEAA 411

Query: 401 IDTTDGTKIIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLE 444
           +  T         G VL+R SGTE ++R+  EA+S + ARE  E
Sbjct: 412 LGET---------GRVLLRPSGTEQVVRVMVEAESHDVARESAE 446


Lambda     K      H
   0.317    0.139    0.396 

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: 26
Number of successful extensions: 6
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: 456
Length of database: 455
Length adjustment: 33
Effective length of query: 423
Effective length of database: 422
Effective search space:   178506
Effective search space used:   178506
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 24 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