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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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