GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ackA in Azospirillum brasilense Sp245

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 AZOBR_RS29810 AZOBR_RS29810 phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS29810 AZOBR_RS29810
           phosphoribosylglycinamide formyltransferase
          Length = 389

 Score =  391 bits (1004), Expect = e-113
 Identities = 208/383 (54%), Positives = 263/383 (68%), Gaps = 5/383 (1%)

Query: 14  RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73
           +++LLGSGELGKE  I  +RLG EVIA D YA+APAM VA  + V +MLD DALR  +  
Sbjct: 5   KILLLGSGELGKEFVIAAKRLGCEVIACDSYANAPAMQVADAAEVFSMLDPDALRAAIAK 64

Query: 74  EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133
             P +IVPE+EAI T++L + E+ GL VVP ARA  +TMNR+ IR +AA EL L TS YR
Sbjct: 65  HTPDFIVPEVEAIRTEVLHEFEDAGLTVVPSARAATMTMNRDRIREVAAVELGLRTSKYR 124

Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193
           +A+S           G PC++KPVMSSSGKGQ+ +R+AE+L  AW YA    R    +VI
Sbjct: 125 YAESLEEVIAGTEHTGLPCVIKPVMSSSGKGQSTVRTAEELEAAWTYAVANMRGDRRKVI 184

Query: 194 VEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARK 253
           VE  V F++EITLLTV   +G+ FC P+GHRQE GDY+ESWQP  M    L+ A+++A K
Sbjct: 185 VEEFVPFEYEITLLTVRTREGILFCEPIGHRQERGDYQESWQPVPMPTALLDDAKDMAAK 244

Query: 254 VVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVG 313
           VV  LGGYG+FGVE FV  DEV+FSE+SPRPHDTGMVTL+SQ+LSEF LH RA LGLP+ 
Sbjct: 245 VVDNLGGYGIFGVEFFVTKDEVVFSELSPRPHDTGMVTLLSQNLSEFDLHARAILGLPIP 304

Query: 314 GIRQYGPAASAVILPQLTSQNVTFDNVQNA--VGA---DLQIRLFGKPEIDGSRRLGVAL 368
            I   GPAASAVIL    ++    + + +A  VG+   D+ +RLFGKP    +RR+GVAL
Sbjct: 305 AIHVRGPAASAVILADREAERFAIEGLADAMRVGSAEHDVDVRLFGKPTTRKNRRMGVAL 364

Query: 369 ATAESVVDAIERAKHAAGQVKVQ 391
           A      DA ERA  AA  + ++
Sbjct: 365 AAGTDTDDARERALKAASAISIR 387


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: 394
Number of extensions: 14
Number of successful extensions: 2
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: 389
Length adjustment: 31
Effective length of query: 361
Effective length of database: 358
Effective search space:   129238
Effective search space used:   129238
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 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