GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_2990
          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:

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