GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Desulfovibrio vulgaris Hildenborough

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate 206109 DVU0685 phosphomannomutase

Query= BRENDA::P26276
         (463 letters)



>MicrobesOnline__882:206109
          Length = 453

 Score =  395 bits (1014), Expect = e-114
 Identities = 204/446 (45%), Positives = 279/446 (62%), Gaps = 4/446 (0%)

Query: 9   LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQL 68
           L A +FRAYDIRG+V      E    +GRA G+  ++ G     VG D R S P     L
Sbjct: 4   LSAHVFRAYDIRGIVDTDFDPEWVERLGRACGTYFVSHGHGAAVVGFDCRHSSPAYHDAL 63

Query: 69  IQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLAN 128
           ++GL+  G  V+ VGMVPTPVLY+A   L  K+GVM+T SHNP +YNGFK+V    T+  
Sbjct: 64  VRGLLSTGVDVTSVGMVPTPVLYFAVKHLGRKAGVMITASHNPSEYNGFKVVAGESTIHG 123

Query: 129 EQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIA 188
           E+I+ + E  E+ + ASG G     DI+P Y + I  D+  A+ +KVVVD GNG  G + 
Sbjct: 124 EEIRRIWEVFERGEFASGHGIGCSHDIVPSYIEAITSDVHPARKLKVVVDGGNGAGGELC 183

Query: 189 PQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRV 248
            +++  LG  V+  +CE DG+FPNHHPDP    N+  L+ +V+ E ADLG+  DGD DR+
Sbjct: 184 VEVLRRLGVEVVAQFCEPDGDFPNHHPDPVVEANMTALMERVQVERADLGIGLDGDADRL 243

Query: 249 GVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGH 308
           G V   G ++  D LL L+A+++++R PG  +I DVKC+ RL   I  +GG+P+MW TGH
Sbjct: 244 GAVDGMGRLLNGDELLSLYAREMLARRPGETVIADVKCSHRLFDDIEAHGGKPMMWITGH 303

Query: 309 SLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFP 368
           S++K +M E GA LAGE+SGH+FF +RWFGFDD IY AARL+E+L+        +   +P
Sbjct: 304 SVVKARMLEVGAPLAGELSGHMFFGDRWFGFDDAIYGAARLVELLAASDVPLTDL-PGWP 362

Query: 369 SDISTPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGWGLVRASNTTP 427
              +T E+++   E +KF ++   Q  A + E   I  +DG RV +P GWGLVRASNT P
Sbjct: 363 PSHATRELHLPCPEHAKFEVVRRAQ--AYFRERCTINDIDGARVIFPDGWGLVRASNTQP 420

Query: 428 VLVLRFEADTEEELERIKTVFRNQLK 453
           VLVLRFEA T E L  I+      L+
Sbjct: 421 VLVLRFEAQTPERLAEIRAFVEEPLR 446


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: 591
Number of extensions: 35
Number of successful extensions: 2
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: 453
Length adjustment: 33
Effective length of query: 430
Effective length of database: 420
Effective search space:   180600
Effective search space used:   180600
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: 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