GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Collimonas arenae Ter10

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 WP_061533943.1 CAter10_RS14415 formate-dependent phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>NCBI__GCF_001584165.1:WP_061533943.1
          Length = 403

 Score =  438 bits (1126), Expect = e-127
 Identities = 240/393 (61%), Positives = 284/393 (72%), Gaps = 8/393 (2%)

Query: 4   LGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLD 63
           LGT L P+AT+VMLLGSGELGKEV I  QRLGVEVIAVDRY +AP   VAHRSHVINM D
Sbjct: 7   LGTPLSPSATKVMLLGSGELGKEVIISLQRLGVEVIAVDRYPNAPGHQVAHRSHVINMAD 66

Query: 64  GDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEG-LNVVPCARATKLTMNREGIRRLAA 122
           G AL  ++  EKP  IVPEIEAIAT+ L+ LE  G + V+P ARA  LTMNREGIRRLA 
Sbjct: 67  GAALEALIAQEKPDLIVPEIEAIATETLVALEAAGKVTVIPTARAAWLTMNREGIRRLAG 126

Query: 123 EELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQ 182
           E L L TS YRFA++ +  + A A+IG+PC++KPVMSSSGKGQ+ I  A+++  AW YA 
Sbjct: 127 ETLALATSPYRFANNLAELKAACAEIGFPCVIKPVMSSSGKGQSKIDGADEVEAAWAYAA 186

Query: 183 QGGRAGAGRVIVEGVVKFDFEITLLTVSAVD-----GVHFCAPVGHRQEDGDYRESWQPQ 237
            GGR  +GRVIVEG + FD+EITLLTV A++       HFC P+GH Q  GDY ESWQP 
Sbjct: 187 AGGRVDSGRVIVEGFIDFDYEITLLTVRALEQDGSIATHFCEPIGHVQVQGDYVESWQPH 246

Query: 238 QMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDL 297
            M P AL +A++IA+KV   LGG GLFGVELFV  D V FSEVSPRPHDTGMVT+ SQ  
Sbjct: 247 PMHPDALLKARDIAKKVTDNLGGLGLFGVELFVKNDMVWFSEVSPRPHDTGMVTMASQQQ 306

Query: 298 SEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAV-GADLQIRLFGKP 356
           SEF LH +A LGLPV  +    PAASAVI  Q  ++ + F+ V +A+ G  + IRLFGKP
Sbjct: 307 SEFELHAKAILGLPV-NVALRSPAASAVIYGQHDAKGIAFEGVADAMRGPGVDIRLFGKP 365

Query: 357 EIDGSRRLGVALATAESVVDAIERAKHAAGQVK 389
           E    RR+GVALATA+ V  A  RAK AA +VK
Sbjct: 366 ESFARRRMGVALATADDVETARTRAKQAAAKVK 398


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: 462
Number of extensions: 18
Number of successful extensions: 5
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: 403
Length adjustment: 31
Effective length of query: 361
Effective length of database: 372
Effective search space:   134292
Effective search space used:   134292
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 24 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