GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Desulfovibrio vulgaris Hildenborough

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 206121 DVU0697 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Query= BRENDA::P07874
         (481 letters)



>MicrobesOnline__882:206121
          Length = 472

 Score =  384 bits (986), Expect = e-111
 Identities = 210/470 (44%), Positives = 286/470 (60%), Gaps = 16/470 (3%)

Query: 4   VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPL-LVCNKEHRFI 62
           +IL+GGSG+RLWP+SR  +PKQ +AL GD TL Q+T+KR         + +V N+EH F 
Sbjct: 11  IILAGGSGTRLWPISRSLFPKQLIALNGDLTLLQETLKRALTHFRPDHIHVVTNEEHVFE 70

Query: 63  VQEQLEAQNLASQA-ILLEPFGRNTAPAVAI---AAMKLVAEGRDELLLILPADHVIEDQ 118
           V+ Q    +   +A ++ EP GRNT PA+ +   AA +         + + P+DH++ D 
Sbjct: 71  VRAQARTLDPRLEAGVIAEPRGRNTLPAILLGLDAAWRATGGETPPTIAVFPSDHMLGDI 130

Query: 119 RAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDE 178
             +Q AL  AT  A+ G  V FG+P + PETGYGYIR      + +    V+ FVEKPD 
Sbjct: 131 PRWQAALDEATRLADDGWFVTFGVPPTHPETGYGYIRRGDS--IADRSFEVEGFVEKPDH 188

Query: 179 ARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAA 238
           A A  ++  G Y+WNSGMF+F     +E +  H +D+           +  GD   I+  
Sbjct: 189 ATATAYLKDGRYFWNSGMFVFNGQSLIEAVHAHQSDLGHWW-------ESRGDRPLIEGY 241

Query: 239 TFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHD 298
           T    P  S+DY +ME  SR  VV    GW+D+GSW +++ +  KD +G V +GD +  D
Sbjct: 242 T--SIPSISVDYGIMEHASRIAVVEADFGWDDLGSWEALYRLGKKDESGCVRRGDTMALD 299

Query: 299 SHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358
             N ++   G  +  IGL+DIV V+T+DA ++   D+ Q VK VV+ L A+  S  + H 
Sbjct: 300 CENSMLFSRGGKLVGIGLKDIVAVQTRDATLVCALDKTQRVKDVVELLKAESSSLAEVHL 359

Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418
            V+RPWGSY  ++ G  F++K ITV PGARLSLQMHHHR+EHW+VVSG A V   +   L
Sbjct: 360 TVHRPWGSYTVLEEGKLFKIKRITVLPGARLSLQMHHHRSEHWVVVSGAALVQVGETETL 419

Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468
           LTENQ   IP  ++HRL+NPGKIPLE+IEVQSG YL EDDI R EDVYGR
Sbjct: 420 LTENQWAVIPRGAMHRLSNPGKIPLELIEVQSGPYLEEDDIVRFEDVYGR 469


Lambda     K      H
   0.319    0.134    0.400 

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: 628
Number of extensions: 32
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: 481
Length of database: 472
Length adjustment: 33
Effective length of query: 448
Effective length of database: 439
Effective search space:   196672
Effective search space used:   196672
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 (21.8 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