GapMind for catabolism of small carbon sources

 

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

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate N515DRAFT_2990 N515DRAFT_2990 phosphomannomutase / phosphoglucomutase

Query= BRENDA::P26276
         (463 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2990 N515DRAFT_2990
           phosphomannomutase / phosphoglucomutase
          Length = 779

 Score =  553 bits (1424), Expect = e-161
 Identities = 270/459 (58%), Positives = 337/459 (73%), Gaps = 3/459 (0%)

Query: 8   TLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQ 67
           T+  +IFRAYD+RG+VG +L  + A  +G++IG+    +G   + VGRDGRLSGPEL   
Sbjct: 321 TVDPTIFRAYDVRGIVGKSLNTDVARLLGQSIGTVMREKGLREIVVGRDGRLSGPELTAA 380

Query: 68  LIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLA 127
           L  GL + G  V D+G VPTPV+YYAA      SGV +TGSHNPPDYNGFKIVV GETL+
Sbjct: 381 LSDGLREAGIDVIDIGAVPTPVVYYAAYRFNTGSGVAVTGSHNPPDYNGFKIVVGGETLS 440

Query: 128 NEQIQALRERIEKNDLA-SGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGV 186
              IQ L  RI  N+L   G GS+ Q+D++P Y ++I  D+   + MKVVVDCGNG+ G 
Sbjct: 441 EGSIQDLYRRIAANELERGGKGSLRQIDVVPDYVERITSDVQAGRRMKVVVDCGNGIPGS 500

Query: 187 IAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGD 246
           +APQ++E +GC VI LYC+VDG FPNHHPDP  P NL+DLI  VK+  ADLG+AFDGDGD
Sbjct: 501 VAPQVLEGIGCEVIQLYCDVDGTFPNHHPDPSDPHNLEDLILAVKSTGADLGVAFDGDGD 560

Query: 247 RVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKT 306
           R+GVVT TG II+PDR LMLFA+DV+SR PGA II+DVKCT  L   I   GG P+MW+T
Sbjct: 561 RLGVVTKTGEIIFPDRTLMLFARDVLSRQPGATIIYDVKCTGHLKGQILDAGGSPLMWRT 620

Query: 307 GHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILS--QDQRDSEHVF 364
           GHSLIK KM+ETGA LAGEMSGH FFKERW+GFDDGIY+ ARLLEIL+   D+R  E +F
Sbjct: 621 GHSLIKSKMRETGAELAGEMSGHFFFKERWYGFDDGIYAGARLLEILAGDLDERTPEQIF 680

Query: 365 SAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASN 424
           +  P  +STPE+ I + E   +  IE  ++ A +G+  +TT+DGVR D+P GWGLVR SN
Sbjct: 681 ATCPKGVSTPELKIEMKEGEHYKFIEKFRQSASFGDAALTTIDGVRADWPDGWGLVRPSN 740

Query: 425 TTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           TTP+LVLRF+AD +  L+RI+ VFR QL AVD +L +PF
Sbjct: 741 TTPILVLRFDADNDAALKRIQNVFREQLHAVDPALKLPF 779


Lambda     K      H
   0.319    0.138    0.410 

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: 945
Number of extensions: 33
Number of successful extensions: 3
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: 463
Length of database: 779
Length adjustment: 37
Effective length of query: 426
Effective length of database: 742
Effective search space:   316092
Effective search space used:   316092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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