GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Synechococcus elongatus PCC 7942

Align Formate-dependent phosphoribosylglycinamide formyltransferase; 5'-phosphoribosylglycinamide transformylase 2; Formate-dependent GAR transformylase; GAR transformylase 2; GART 2; Non-folate glycinamide ribonucleotide transformylase; Phosphoribosylglycinamide formyltransferase 2; EC 2.1.2.- (characterized)
to candidate Synpcc7942_0588 Synpcc7942_0588 phosphoribosylglycinamide formyltransferase 2

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__SynE:Synpcc7942_0588
          Length = 391

 Score =  387 bits (993), Expect = e-112
 Identities = 213/380 (56%), Positives = 263/380 (69%), Gaps = 2/380 (0%)

Query: 14  RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73
           R+MLLGSGELGKE AI  QRLG  VIAVDRYA APAM VA  S VI+MLDG+AL  VV+ 
Sbjct: 10  RLMLLGSGELGKEFAIAAQRLGNTVIAVDRYAHAPAMQVADASAVISMLDGEALEAVVQE 69

Query: 74  EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133
            +P  I+PEIEAI T+ L + E+ GL V+P ARAT  TMNR+ IR LAA++L L T+ Y 
Sbjct: 70  FQPDLIIPEIEAIRTEKLQEFEDRGLTVIPTARATHFTMNRDRIRDLAAQQLGLRTARYA 129

Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193
           +A      +   A IGYP ++KPVMSSSGKGQ+ I+  +QL  AW YA  G R  + +VI
Sbjct: 130 YASCFEELQTVAAAIGYPNVIKPVMSSSGKGQSIIQQPDQLQAAWDYAIAGSRGDSQKVI 189

Query: 194 VEGVVKFDFEITLLTVSAVDG-VHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIAR 252
           +E  + F+ EITLLT+    G   FC P+GHRQE GDY+ESWQP  + P  L +AQ IA 
Sbjct: 190 LEEFIPFELEITLLTIRQWQGPTLFCPPIGHRQERGDYQESWQPAPLRPDLLAQAQAIAA 249

Query: 253 KVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPV 312
           +V  ALGG GLFGVE FV  DEVIFSE+SPRPHDTGMVTLISQ+L+EF LH+RA LGLP+
Sbjct: 250 QVTEALGGAGLFGVEFFVTPDEVIFSELSPRPHDTGMVTLISQNLNEFELHLRAVLGLPI 309

Query: 313 GGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGAD-LQIRLFGKPEIDGSRRLGVALATA 371
             I   GP+AS VIL + +    ++  V  A+    + +RLFGKP++   RR+GVALA  
Sbjct: 310 PAIELLGPSASRVILAEDSGDRPSYAGVAAALQEPWVDLRLFGKPDMRPQRRMGVALARD 369

Query: 372 ESVVDAIERAKHAAGQVKVQ 391
           ESV  A  +A  AA QV +Q
Sbjct: 370 ESVEAARAKADRAASQVTIQ 389


Lambda     K      H
   0.320    0.136    0.390 

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: 410
Number of extensions: 15
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: 392
Length of database: 391
Length adjustment: 31
Effective length of query: 361
Effective length of database: 360
Effective search space:   129960
Effective search space used:   129960
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: 50 (23.9 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