GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Azospirillum thiophilum BV-S

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_045583071.1 AL072_RS16975 formate-dependent phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>NCBI__GCF_001305595.1:WP_045583071.1
          Length = 389

 Score =  384 bits (986), Expect = e-111
 Identities = 202/383 (52%), Positives = 257/383 (67%), Gaps = 5/383 (1%)

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

Query: 74  EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133
             P YIVPE+EAI T++L + EE G  VVP ARA  +TMNR+ IR +AA EL L TS YR
Sbjct: 65  HHPDYIVPEVEAIRTEVLHEFEEAGTTVVPSARAATMTMNRDRIREVAAAELGLRTSRYR 124

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

Query: 194 VEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARK 253
           VE  V F++EITLLTV   DG+ +C P+GHRQE GDY+ESWQP  M    L+ A+ +A +
Sbjct: 185 VEEFVPFEYEITLLTVRTRDGILYCEPIGHRQERGDYQESWQPVAMPQRMLDDAKAMAAR 244

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

Query: 314 GIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-----ADLQIRLFGKPEIDGSRRLGVAL 368
            I     +ASAVIL    ++    + +  A+       ++ +RLFGKP    +RR+GVAL
Sbjct: 305 SITCRASSASAVILADREAETFRIEGLSGALSLGSAEQEVDVRLFGKPTTRKNRRMGVAL 364

Query: 369 ATAESVVDAIERAKHAAGQVKVQ 391
           A      DA  RAK AA +V ++
Sbjct: 365 AAGSDTDDARARAKQAADKVTIR 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: 376
Number of extensions: 11
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 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