GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Bacteroides clarus YIT 12056

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_009122713.1 BUB52_RS04025 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>NCBI__GCF_900129655.1:WP_009122713.1
          Length = 462

 Score =  254 bits (648), Expect = 5e-72
 Identities = 167/457 (36%), Positives = 248/457 (54%), Gaps = 13/457 (2%)

Query: 6   GTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERP-LVVVGRDTRVSGEMLKDALISG 64
           GT G  G   E + P   +K   A+ TL+++    +   +VVGRD R+SGEM+K+ ++  
Sbjct: 12  GTIG--GGVGEGLNPLDIVKFTSAYATLIRKTCTVKSNKIVVGRDARISGEMVKNVVVGT 69

Query: 65  LLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKER 124
           L+  G DV+D+ +A TP  + A     A GG ++TASHNP ++N +KLL   G  L KE 
Sbjct: 70  LMGMGWDVVDIDLASTPTTELAVTMEGASGGIILTASHNPKQWNALKLLNEKGEFLNKEE 129

Query: 125 EAIVEELFFSEDFHRAKWNEIGELRKE-DIIKPYIEAI--KNRVDVEAIKKRRPFVVVDT 181
              V  +  +E F  A+ +++G  RK+    + +I+++   + VDVEAIKK    V +D 
Sbjct: 130 GNEVLRIAEAEAFDFAEVDKLGSYRKDLTYNQKHIDSVLALDLVDVEAIKKAGFRVAIDC 189

Query: 182 SNGAGSLTLPYLLRELGCK-VVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240
            N  G + LP LL +LG + V  +   P G+F   NPEP E+NL   M ++K   AD   
Sbjct: 190 VNSVGGIILPQLLEQLGVQHVEKLYCEPTGNF-QHNPEPLEKNLGDIMNLMKGGKADVAF 248

Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDIAKRNGA 300
             D D DR   I E+G+    + T   VAD VL+   G   V+ ++++  L D+ ++   
Sbjct: 249 VVDPDVDRLAMICEDGKMYGEEYTLVTVADYVLKHTPGN-TVSNLSSTRALRDVTRKYDQ 307

Query: 301 KVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKKF 360
           +   + VG++ V   + E    IGGE NGGVI+P    GRD  +  A  +   A  GKK 
Sbjct: 308 QYYASAVGEVNVTTKMKEVGAVIGGEGNGGVIYPASHYGRDALVGIALFLSHLAHEGKKV 367

Query: 361 SELIDELPKYYQFKTKRHV--EGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDGWVLV 418
           SEL    P Y+  K +  +  + D  AI+AKV E+   K  +I+  DG KI F D WV +
Sbjct: 368 SELRATYPAYFMAKNRVDLTPDTDVDAILAKVKEI--YKNEEINDIDGVKIDFPDKWVHL 425

Query: 419 RASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEALK 455
           R S TEPIIR++SEA + E A E     +K++E+  K
Sbjct: 426 RKSNTEPIIRVYSEAATPEAAEEIGRQIMKVIEDLAK 462


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: 517
Number of extensions: 32
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: 456
Length of database: 462
Length adjustment: 33
Effective length of query: 423
Effective length of database: 429
Effective search space:   181467
Effective search space used:   181467
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.

Links

Downloads

Related tools

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