GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Synechococcus elongatus PCC 7942

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate Synpcc7942_1608 Synpcc7942_1608 mannose-1-phosphate guanylyltransferase (GDP)

Query= BRENDA::P07874
         (481 letters)



>FitnessBrowser__SynE:Synpcc7942_1608
          Length = 469

 Score =  544 bits (1401), Expect = e-159
 Identities = 271/470 (57%), Positives = 337/470 (71%), Gaps = 3/470 (0%)

Query: 1   MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPLLVCNKEH 59
           ++PVILSGGSGSRLWPLSR+ YPKQF AL  D +L Q+T+ RL    G+ +PLL+CN++H
Sbjct: 2   LVPVILSGGSGSRLWPLSRESYPKQFHALLSDYSLLQETLLRLEGLPGLASPLLICNEQH 61

Query: 60  RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119
           RF+V E L A    + AI+LEP GRNTAPAVAIAA++  ++G D LLL+LP+DH I D  
Sbjct: 62  RFLVAEHLRAIGQTAAAIVLEPEGRNTAPAVAIAALQAQSQGEDPLLLVLPSDHSIADPA 121

Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179
           AF+  +  A   A  G +V FGI    PETGYGYI+A +D  L  G   +  F+EKP+ A
Sbjct: 122 AFRATVQTAIALATAGHLVTFGIVPEAPETGYGYIKAGSDLDL--GGFAIDRFIEKPNLA 179

Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239
            A  +VA+G YYWNSGMFL RAS YL EL ++  +++  C  A ++ Q D D V +D AT
Sbjct: 180 TAENYVASGCYYWNSGMFLIRASVYLSELARYAPEMFTACEAAWQKRQADLDFVRLDPAT 239

Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299
           F  CP +SIDYAVME T +  V+PL AGW DVGSWSS+W    +D  GNVT GD L  D 
Sbjct: 240 FAQCPSDSIDYAVMEHTQQGAVLPLQAGWTDVGSWSSLWQALEQDGAGNVTVGDSLALDC 299

Query: 300 HNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCE 359
            N  +   G+LV  +GLED+V VET DA++IAH+DR Q VK VV+ L  + R E++ H +
Sbjct: 300 RNVYLRSEGRLVVGVGLEDVVAVETDDALLIAHRDRTQTVKQVVEALQREARRESRAHRK 359

Query: 360 VYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLL 419
           +YRPWG YDS+D+G RFQVK ITV PGA LSLQMHHHRAEHWIVV GTA VT D++  LL
Sbjct: 360 IYRPWGRYDSLDLGDRFQVKRITVNPGASLSLQMHHHRAEHWIVVKGTALVTRDNEEVLL 419

Query: 420 TENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469
           TENQSTYIP+   HRL+NPG++PLE+IEVQSGSYL EDDI R ED YGR+
Sbjct: 420 TENQSTYIPVGCKHRLSNPGRVPLEMIEVQSGSYLEEDDIVRFEDHYGRS 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: 627
Number of extensions: 26
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: 481
Length of database: 469
Length adjustment: 33
Effective length of query: 448
Effective length of database: 436
Effective search space:   195328
Effective search space used:   195328
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