GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ackA in Pseudomonas putida KT2440

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 PP_1457 PP_1457 Phosphoribosylglycinamide formyltransferase 2

Query= SwissProt::P33221
         (392 letters)



>lcl|FitnessBrowser__Putida:PP_1457 PP_1457
           Phosphoribosylglycinamide formyltransferase 2
          Length = 393

 Score =  520 bits (1340), Expect = e-152
 Identities = 270/392 (68%), Positives = 312/392 (79%), Gaps = 1/392 (0%)

Query: 1   MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60
           MT +GT L P ATRV+L G GELGKEV IE QRLGVEVIAVDRYA+APAM VAHRSHV+N
Sbjct: 1   MTRIGTPLSPTATRVLLCGCGELGKEVVIELQRLGVEVIAVDRYANAPAMQVAHRSHVVN 60

Query: 61  MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRL 120
           MLDG ALR V+E EKPHYIVPEIEAIAT  L++LE EG  VVP ARAT+LTMNREGIRRL
Sbjct: 61  MLDGVALRAVIEAEKPHYIVPEIEAIATATLVELENEGFTVVPTARATQLTMNREGIRRL 120

Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180
           AAEEL LPTS Y FAD+   + +AVAD+GYPC+VKPVMSSSGKGQ+ +RS   L ++W Y
Sbjct: 121 AAEELDLPTSPYHFADTYEDYAKAVADLGYPCVVKPVMSSSGKGQSLLRSDADLQKSWDY 180

Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMS 240
           AQ+GGRAG GRVIVEG + F++EITLLTV  V G  F  PVGHRQE GDY+ESWQPQ MS
Sbjct: 181 AQEGGRAGKGRVIVEGFIDFEYEITLLTVRHVGGTTFLEPVGHRQEKGDYQESWQPQAMS 240

Query: 241 PLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF 300
           P AL  +Q +A+ V  ALGG GLFGVELFV GD+V FSEVSPRPHDTG+VTLISQDLS+F
Sbjct: 241 PKALAESQRVAKAVTDALGGRGLFGVELFVKGDQVWFSEVSPRPHDTGLVTLISQDLSQF 300

Query: 301 ALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFGKPEID 359
           ALH RA LGLP+  +RQ+GP+ASAVILP+  SQ  +F N+  A+   D  IRLFGKPEI+
Sbjct: 301 ALHARAILGLPIPVVRQFGPSASAVILPEGQSQQTSFANLGAALSEPDTAIRLFGKPEIN 360

Query: 360 GSRRLGVALATAESVVDAIERAKHAAGQVKVQ 391
           G+RR+GV LA  ESV  A  +A  A+  VKV+
Sbjct: 361 GTRRMGVCLARDESVELARAKATRASQAVKVE 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: 479
Number of extensions: 19
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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