GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Caldicellulosiruptor hydrothermalis 108

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_013402170.1 CALHY_RS01030 phosphoglucosamine mutase

Query= metacyc::MONOMER-13382
         (455 letters)



>NCBI__GCF_000166355.1:WP_013402170.1
          Length = 449

 Score =  267 bits (683), Expect = 5e-76
 Identities = 169/461 (36%), Positives = 253/461 (54%), Gaps = 18/461 (3%)

Query: 1   MGKLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEA 60
           MGKLFGT GVRG+AN+++T E A  +G A G  +  E ++KP +++G+DTR+S +ML+ A
Sbjct: 1   MGKLFGTDGVRGVANKELTCELAFDLGRA-GAYVLTETKQKPKILIGKDTRISCDMLEAA 59

Query: 61  LISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120
           L +GL SVG DV   G+  TPA+    K    D G +I+ASHNP E+NGIK     G  L
Sbjct: 60  LCAGLTSVGADVYLAGVITTPAIAHLVKSHGFDAGIMISASHNPYEFNGIKFFNSQGFKL 119

Query: 121 KKEREAIVEELFFKEDFD---RAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFV 177
             + E  +E++     ++    A++  IG V R D+ K Y E +KS ++  + K  K  +
Sbjct: 120 SDQIEEKIEDIILNRKWNEVPHAQFDAIGRVNRVDLKKNYQEYLKSTLNGASFKGLK--I 177

Query: 178 VVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGAD 237
           V+D +NGA     P +  ELG +V+ +N QPDG     N E    +LK   + V    AD
Sbjct: 178 VIDCANGAAYKIAPEVFEELGAEVVVINNQPDG--TNINKECGSTHLKMLQQEVVKNKAD 235

Query: 238 FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG---GGLLVTTVATSNLLDDI 294
           FG+A DGDADR +F+DE G  + GDK   L+A   LK++G      LV TV ++  L   
Sbjct: 236 FGIAYDGDADRTLFVDEEGSIVDGDKIMLLLAQN-LKQQGKLQRNTLVVTVMSNMGLFVA 294

Query: 295 AKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFA 354
           AK+ G  +  TKVGD  V   + E   +IGGE++G +I  +     DG +T  ++ ++  
Sbjct: 295 AKELGINLEVTKVGDRYVLEKMLEGGYSIGGEQSGHIILLDFATTGDGILTSLQLTKLIK 354

Query: 355 KSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDG 414
           +SGKK S+L   +  Y Q+     VE  +  + +K   +        +  +G       G
Sbjct: 355 ESGKKLSDLAKIMKVYPQVLVNAKVENGKKDLYSKDPVILEAIKKVEEKLNG------KG 408

Query: 415 WVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455
            VL+R SGTEP+IR+  E +  E+ ++  +    L+E  LS
Sbjct: 409 RVLIRPSGTEPLIRVMIEGEDYEEIKKDAHELASLIESRLS 449


Lambda     K      H
   0.317    0.138    0.391 

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: 544
Number of extensions: 25
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: 455
Length of database: 449
Length adjustment: 33
Effective length of query: 422
Effective length of database: 416
Effective search space:   175552
Effective search space used:   175552
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