Alignments for a candidate for ackA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Burkholderia phytofirmans PsJN

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 BPHYT_RS06125 BPHYT_RS06125 phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__BFirm:BPHYT_RS06125
          Length = 404

 Score =  450 bits (1158), Expect = e-131
 Identities = 245/394 (62%), Positives = 285/394 (72%), Gaps = 9/394 (2%)

Query: 4   LGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLD 63
           +GT L  +ATRVMLLG+GELGKEV I  QRLGVEVIAVDRY +AP   VAHR+HVI+M D
Sbjct: 7   IGTPLSESATRVMLLGAGELGKEVIIALQRLGVEVIAVDRYPNAPGHQVAHRAHVIDMTD 66

Query: 64  GDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGL-NVVPCARATKLTMNREGIRRLAA 122
             ALR +VE E+PH IVPEIEAIATD L  +E +GL  V+P ARAT+LTMNREGIRRLAA
Sbjct: 67  RAALRALVEQERPHLIVPEIEAIATDALAAIESDGLAEVIPTARATQLTMNREGIRRLAA 126

Query: 123 EELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQ 182
           EEL LPTS Y FADS    R  +A +GYPC+VKPVMSSSGKGQ+ +RS   +  AW+YA 
Sbjct: 127 EELGLPTSPYAFADSLDELRAGIAKVGYPCVVKPVMSSSGKGQSVLRSDADVEPAWQYAL 186

Query: 183 QGGRAGAGRVIVEGVVKFDFEITLLTVSAVD------GVHFCAPVGHRQEDGDYRESWQP 236
            GGR   GRVIVEG + F++EIT LTV A+D        +FC P+GH Q  GDY ESWQP
Sbjct: 187 AGGRVNHGRVIVEGFIDFEYEITQLTVRAIDPASGEVSTYFCDPIGHVQVAGDYVESWQP 246

Query: 237 QQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQD 296
           Q MSPLALER++E+A KV  ALGG GLFGVELFV GD+V FSEVSPRPHDTG+VTL SQ 
Sbjct: 247 QPMSPLALERSREVAHKVTAALGGRGLFGVELFVRGDDVWFSEVSPRPHDTGLVTLCSQR 306

Query: 297 LSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGA-DLQIRLFGK 355
            SEF LH RA LGLPV    +  P ASAVI   L    + F+ V  A+   +  +RLFGK
Sbjct: 307 FSEFELHARAILGLPVDTSLR-APGASAVIYGGLDEAGIAFEGVAAALAVPNADLRLFGK 365

Query: 356 PEIDGSRRLGVALATAESVVDAIERAKHAAGQVK 389
           PE    RR+GVALAT E+  +A  RAK AA  V+
Sbjct: 366 PESFAKRRMGVALATGENTDEARSRAKQAAAAVR 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: 454
Number of extensions: 15
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: 404
Length adjustment: 31
Effective length of query: 361
Effective length of database: 373
Effective search space:   134653
Effective search space used:   134653
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources