GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SynE:Synpcc7942_1608 Synpcc7942_1608
           mannose-1-phosphate guanylyltransferase (GDP)
          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 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