GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Dechlorosoma suillum PS

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 Dsui_1003 Dsui_1003 phosphoribosylglycinamide formyltransferase 2

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__PS:Dsui_1003
          Length = 410

 Score =  451 bits (1159), Expect = e-131
 Identities = 248/398 (62%), Positives = 288/398 (72%), Gaps = 14/398 (3%)

Query: 4   LGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLD 63
           +GT L P+AT+VMLLG+GELGKEV I  QRLGVEVIAVDRYADAP M VAHRSHVI+M D
Sbjct: 3   IGTPLSPSATKVMLLGAGELGKEVIIALQRLGVEVIAVDRYADAPGMQVAHRSHVISMTD 62

Query: 64  GDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGL-NVVPCARATKLTMNREGIRRLAA 122
           G ALRR++ELEKPH +VPEIEAIATD L+++E EGL  V+P A A KLTMNREGIRRLAA
Sbjct: 63  GAALRRLIELEKPHLVVPEIEAIATDTLVEIEAEGLAQVIPTALAAKLTMNREGIRRLAA 122

Query: 123 EELQLPTSTYRFADSESLFREAV------ADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQ 176
           EEL LPTS YRFADS +  + A+        IGYPC+VKPVMSSSGKGQ+ ++    + +
Sbjct: 123 EELGLPTSPYRFADSLAELQAAIDGTGEEKGIGYPCVVKPVMSSSGKGQSLLKGPADVEK 182

Query: 177 AWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDG-----VHFCAPVGHRQEDGDYR 231
           AW +AQ GGR    RVIVEG VKFD+EIT LTV AV         FC P+GH Q DGDY 
Sbjct: 183 AWNHAQAGGRVQQSRVIVEGFVKFDYEITQLTVRAVGSSGQVETFFCEPIGHIQVDGDYV 242

Query: 232 ESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVT 291
           ESWQPQ MS  A E+++EIA KV   LGG G+FGVELF+ GD+V FSEVSPRPHDTG+VT
Sbjct: 243 ESWQPQPMSEAAREKSREIAEKVTSNLGGRGIFGVELFIKGDQVWFSEVSPRPHDTGLVT 302

Query: 292 LISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGA-DLQI 350
           L SQ LSEF LH RA LGLPV    +  P ASAVI   L  Q V ++ V  A+      +
Sbjct: 303 LTSQRLSEFELHARAILGLPVDASLR-TPGASAVIYGGLEEQGVAYEGVAEALQVPTADL 361

Query: 351 RLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQV 388
           RLFGKPE    RR+GVALAT  S+  A +RA  AA +V
Sbjct: 362 RLFGKPESFKKRRMGVALATGGSIEQARQRASLAASRV 399


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: 501
Number of extensions: 21
Number of successful extensions: 6
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: 410
Length adjustment: 31
Effective length of query: 361
Effective length of database: 379
Effective search space:   136819
Effective search space used:   136819
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