GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Acidovorax sp. GW101-3H11

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 Ac3H11_4666 Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4666
          Length = 400

 Score =  412 bits (1058), Expect = e-119
 Identities = 235/398 (59%), Positives = 274/398 (68%), Gaps = 13/398 (3%)

Query: 1   MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60
           MT LGT L P AT+VMLLGSGELGKEV I  QRLGVE IAVDRY +AP   VAH +  I 
Sbjct: 1   MTTLGTPLSPHATKVMLLGSGELGKEVLIALQRLGVETIAVDRYDNAPGQQVAHHARTIT 60

Query: 61  MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEG-LNVVPCARATKLTMNREGIRR 119
           M D   L+ ++E E+PH +VPEIEAIAT ML +LE  G + V+P ARA +LTM+REGIR 
Sbjct: 61  MSDPAQLKALIEAERPHLVVPEIEAIATPMLEELEAAGTVRVIPTARAARLTMDREGIRV 120

Query: 120 LAAEELQLPTSTYRFADSESLFREAV-ADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAW 178
           LAAE L LPTS Y+F +S    + A+ A IGYPCIVKPVMSSSGKGQ+ I   E + +AW
Sbjct: 121 LAAETLGLPTSPYKFCNSLEELQAAIDAGIGYPCIVKPVMSSSGKGQSKIDVPEDVQKAW 180

Query: 179 KYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDG-----VHFCAPVGHRQEDGDYRES 233
            YA  GGR   GRVIVEG + FD+EIT LTV +V         FC P+GH Q  GDY ES
Sbjct: 181 DYAMAGGRVSHGRVIVEGFIDFDYEITQLTVRSVGAEGQIVTSFCDPIGHVQVSGDYVES 240

Query: 234 WQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLI 293
           WQP  M P ALE++++IA+ V   LGG GLFGVELFV G+ V FSEVSPRPHDTG+VTL 
Sbjct: 241 WQPHPMHPAALEKSRQIAKAVTDNLGGQGLFGVELFVKGENVWFSEVSPRPHDTGLVTLC 300

Query: 294 SQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAV---GADLQI 350
           +Q  SEF LH RA LGLPV   R   P ASAVI   + +Q + FD V+ A+   G DL  
Sbjct: 301 TQHQSEFELHARAILGLPV-DTRLRNPGASAVIYGGVEAQGIVFDGVEEALRVPGTDL-- 357

Query: 351 RLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQV 388
           RLFGKPE    RR+GVALA AE V  A   AK AAG+V
Sbjct: 358 RLFGKPESFVKRRMGVALARAEDVDTARHNAKLAAGKV 395


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: 442
Number of extensions: 23
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: 400
Length adjustment: 31
Effective length of query: 361
Effective length of database: 369
Effective search space:   133209
Effective search space used:   133209
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