GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_879 Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_879
          Length = 393

 Score =  517 bits (1331), Expect = e-151
 Identities = 264/392 (67%), Positives = 312/392 (79%), Gaps = 1/392 (0%)

Query: 1   MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60
           MT +GT L P ATRV++ G GELGKEV IE QRLGVEVIAVDRYA+APAM VAHRSHVIN
Sbjct: 1   MTRIGTPLSPTATRVLMCGCGELGKEVVIELQRLGVEVIAVDRYANAPAMQVAHRSHVIN 60

Query: 61  MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRL 120
           MLDG ALR V+E EKPH+IVPEIEAIAT  L++LE EG  V+P ARATKLTMNREGIRRL
Sbjct: 61  MLDGAALRAVIEAEKPHFIVPEIEAIATATLVELESEGFTVIPTARATKLTMNREGIRRL 120

Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180
           AAEEL LPTS Y FAD+   + +AV D+G+PC+VKPVMSSSGKGQ+ +RS + + +AW Y
Sbjct: 121 AAEELGLPTSPYYFADTFEDYSKAVDDLGFPCVVKPVMSSSGKGQSLLRSVDDVRKAWDY 180

Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMS 240
           AQ+GGRAG GRVI+EG + FD+EITLLTV  V G  FCAPVGHRQE GDY+ESWQPQ MS
Sbjct: 181 AQEGGRAGKGRVIIEGFIDFDYEITLLTVRHVGGTTFCAPVGHRQEKGDYQESWQPQAMS 240

Query: 241 PLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF 300
           P+AL  ++ +A+ V  ALGG GLFGVELF+ GD+V FSEVSPRPHDTG+VTLISQDLS+F
Sbjct: 241 PVALAESERVAKAVTEALGGRGLFGVELFIKGDQVWFSEVSPRPHDTGLVTLISQDLSQF 300

Query: 301 ALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFGKPEID 359
           ALH RA LGLP+  IRQ+GP+ASAVIL +  S    F N+  A+G  D  +RLFGKPE++
Sbjct: 301 ALHARAILGLPIPLIRQFGPSASAVILVEGQSTQTAFANLGAALGEPDTALRLFGKPEVN 360

Query: 360 GSRRLGVALATAESVVDAIERAKHAAGQVKVQ 391
           G RR+GVALA  ES+  A  +A  A+  V V+
Sbjct: 361 GQRRMGVALARDESIEAARAKATRASQAVVVE 392


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: 487
Number of extensions: 15
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: 393
Length adjustment: 31
Effective length of query: 361
Effective length of database: 362
Effective search space:   130682
Effective search space used:   130682
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