GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Marivita geojedonensis DPG-138

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_085636384.1 MGEO_RS08970 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>NCBI__GCF_002115805.1:WP_085636384.1
          Length = 447

 Score =  212 bits (539), Expect = 2e-59
 Identities = 154/447 (34%), Positives = 224/447 (50%), Gaps = 34/447 (7%)

Query: 3   KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           KLFGT GVRG AN   +T + AL+IG A G   +++ +    VV+G+DTR SG M ++AL
Sbjct: 4   KLFGTDGVRGTANAYPMTADMALRIGAAVGRHFRQDSKGVHRVVIGKDTRQSGYMFENAL 63

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

Query: 122 KEREAIVEELF-------FSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKKRR 174
              EA +E L         +E+  RAK  + G  R ++ +K    A    + ++ +K   
Sbjct: 124 DADEAEIEALIETGVEPAQAENIGRAKRIDDGRFRYQERVKSTFPA---DLRLDGLK--- 177

Query: 175 PFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKAL 234
             VV+D +NGA     P +L ELG  V+ +   P+G             L      V A 
Sbjct: 178 --VVIDCANGAAYKAAPEVLWELGADVIPLGVTPNGSNINEGCGSTHPQLAA--AAVVAH 233

Query: 235 GADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLREN--GGGLLVTTIATSNLLD 292
           GAD G+  DGDADR + IDE G+   GD+  AL+A     E     G+LV T+ ++  L+
Sbjct: 234 GADIGICLDGDADRVILIDETGQVADGDQIMALMAARWAEEQRLRDGVLVATVMSNLGLE 293

Query: 293 DIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEI 352
                 G ++ RT VGD  V  A+      +GGE++G ++  D+    DG M   + +  
Sbjct: 294 RFLDGRGLRLERTGVGDRYVVEAMRRGGWNLGGEQSGHIVMTDYATTGDGLMAGLQFLGE 353

Query: 353 FAKSGKKFSEL---IDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKI 409
             ++GK  S L    D +P+       ++V  D       VA L E    K    D    
Sbjct: 354 MCRTGKPASALARSFDPVPQLL-----KNVRYD-----PSVAPL-ETASVKAAIADAEAR 402

Query: 410 IFDDGWVLVRASGTEPIIRIFSEAKSE 436
           +   G +L+R SGTEP+IR+ +E + E
Sbjct: 403 LNGSGRLLIRKSGTEPLIRVMAECEDE 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: 534
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 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