GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Dinoroseobacter shibae DFL-12

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 3609008 Dshi_2397 phosphoglucosamine mutase (RefSeq)

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Dino:3609008
          Length = 447

 Score =  214 bits (544), Expect = 6e-60
 Identities = 156/454 (34%), Positives = 227/454 (50%), Gaps = 48/454 (10%)

Query: 3   KLFGTFGVRGIANEE-ITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           KLFGT GVRG AN   +T E AL++G A G   +R+      VV+G+DTR+SG M + AL
Sbjct: 4   KLFGTDGVRGTANTAPMTAEMALRLGAAAGRYFRRDQSAAHRVVIGKDTRLSGYMFETAL 63

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +G  STG +V+ +G  PTPA+   T    AD G +I+ASHNP + NGIK   P+G  L 
Sbjct: 64  TAGFTSTGMNVLLLGPIPTPAVALLTQSMRADVGVMISASHNPADDNGIKFFGPDGYKLS 123

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKN----RVDVEAIKKRRPF 176
              E  +EE+  + D   A+   IG  ++ +D +  YIE  K      + ++ +K     
Sbjct: 124 DAAEEEIEEI-LAGDIRPAQAPNIGRAKRIDDGLGRYIERAKRTFPAHLRLDGLK----- 177

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236
           VVVD +NGA     P +L ELG  V+ V   P+G     N +      +   E V + GA
Sbjct: 178 VVVDCANGAAYKVAPAVLWELGADVIPVGVSPNGR--NINRDCGSTAPQTAAEAVVSHGA 235

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFAL-----VADAVLRENGGGLLVTTIATSNLL 291
           D G+  DGDADR + +DENG    GD+  AL      A  +LR+N    LV T+ ++  L
Sbjct: 236 DVGICLDGDADRVMILDENGELADGDQLMALFATRWAAQGLLRDN---TLVATVMSNLGL 292

Query: 292 DDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVE 351
           +      G K++RT VGD  V  A+ +    +GGE++G ++  D     DG M   + + 
Sbjct: 293 EYYLNDLGLKLVRTAVGDRYVVEAMRKGGWNLGGEQSGHIVMLDHGTTGDGLMAGLQFLA 352

Query: 352 IFAKSGKKFSELIDELPKYYQ-FKTKRHVEGD--------RKAIVAKVAELAEKKGYKID 402
              + G+  SEL        Q  +  R   G         + AI A  A+L+ K      
Sbjct: 353 EMVQQGRSASELKHSFTTVPQRLENVRFGAGQDPLAAASVKSAIAAAEAQLSGK------ 406

Query: 403 TTDGTKIIFDDGWVLVRASGTEPIIRIFSEAKSE 436
                      G +L+R SGTEP++R+ +E + E
Sbjct: 407 -----------GRLLIRKSGTEPLVRVMAECEDE 429


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: 527
Number of extensions: 29
Number of successful extensions: 7
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: 447
Length adjustment: 33
Effective length of query: 423
Effective length of database: 414
Effective search space:   175122
Effective search space used:   175122
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