GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Dyella japonica UNC79MFTsu3.2

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate N515DRAFT_1372 N515DRAFT_1372 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1372
          Length = 450

 Score =  190 bits (483), Expect = 7e-53
 Identities = 146/455 (32%), Positives = 222/455 (48%), Gaps = 17/455 (3%)

Query: 3   KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRE-RPLVVVGRDTRVSGEMLKDA 60
           K FGT G+RG +    I+ +F L++G A G  L R+ RE RP V++G+DTRVSG M + A
Sbjct: 5   KYFGTDGIRGPVGQWPISADFMLRLGRAAGMALARDTREGRPKVLIGKDTRVSGYMFEAA 64

Query: 61  LISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120
           L +GL++ G DV  +G  PTPA+ + T    A  G VI+ASHNP + NGIK     G  L
Sbjct: 65  LEAGLVAAGVDVGLLGPMPTPAVAFLTRSLRAQAGIVISASHNPHQDNGIKFFSAIGEKL 124

Query: 121 KKEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRVDVEAIKKRRPFVVV 179
             + EA + EL    +F       +G+  R +D    YIE  K  +       R   +V+
Sbjct: 125 SDDVEAAI-ELGLDAEFTTEAPERLGKASRIDDAGGRYIEFCKRTLVDSEFTLRGLRIVL 183

Query: 180 DTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFG 239
           D +NGA     P +  ELG +V+++   PDG     N      + +     V    AD G
Sbjct: 184 DCANGATYQVAPKVFAELGAEVIAIGHKPDGF--NINRGVGSTHPQTLQLAVLEHHADIG 241

Query: 240 VAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG-GGLLVTTIATSNLLDDIAKRN 298
           +A DGD DR   +D  G    GD    ++A A   +    G +V T+ ++  L       
Sbjct: 242 IAFDGDGDRVQLVDREGVLADGDDMLFILARAWAAQGRLKGPVVGTLMSNYGLQQALAAL 301

Query: 299 GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGK 358
              ++R  VGD  V + L E+ G +GGE +G ++  D     DG ++   ++E  A  G+
Sbjct: 302 DVDLIRANVGDRYVLQKLKEHGGQLGGETSGHILCLDRATTGDGIVSALAVLE--ALGGR 359

Query: 359 KFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDGWVLV 418
             +E    L K  Q        G R+++ +      E K    +T +  +     G V++
Sbjct: 360 DLAEARQGLYKMPQIMINVRANGARESLHSD-----EVKQALAETEEALR---GRGRVVL 411

Query: 419 RASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEA 453
           RASGTEP++R+  EA  E + R   E   ++++ A
Sbjct: 412 RASGTEPLVRVTVEAADEAEVRRMAEQLAEVVKSA 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: 504
Number of extensions: 28
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: 450
Length adjustment: 33
Effective length of query: 423
Effective length of database: 417
Effective search space:   176391
Effective search space used:   176391
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