GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Pseudomonas stutzeri RCH2

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 GFF3079 Psest_3137 phosphoribosylglycinamide formyltransferase 2

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__psRCH2:GFF3079
          Length = 393

 Score =  493 bits (1270), Expect = e-144
 Identities = 256/392 (65%), Positives = 301/392 (76%), Gaps = 1/392 (0%)

Query: 1   MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60
           M  +GT L P+ATRV+L G GELGKE+ IE QRLGVEVIAVDRYA+APAM VAHRSHVI+
Sbjct: 1   MPRIGTPLSPSATRVLLCGCGELGKELVIELQRLGVEVIAVDRYANAPAMQVAHRSHVID 60

Query: 61  MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRL 120
           MLDG ALR V+E E+PHYIVPEIEAIAT  L++LE+EG +V+P ARA +LTMNREGIRRL
Sbjct: 61  MLDGAALRSVIEQERPHYIVPEIEAIATATLVELEQEGYSVIPTARAAQLTMNREGIRRL 120

Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180
           AAEEL LPTS YRFADS    R A   +G+PC++KPVMSSSGKGQ+ +RS   +  AW Y
Sbjct: 121 AAEELGLPTSPYRFADSLDECRTAARALGFPCLIKPVMSSSGKGQSVLRSEADIDAAWDY 180

Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMS 240
           AQ GGRAG GRVIVEG + FD+EITLLTV    G  FC PVGHRQE GDY+ESWQPQ M 
Sbjct: 181 AQAGGRAGRGRVIVEGFIDFDYEITLLTVRHAGGTSFCEPVGHRQEKGDYQESWQPQPME 240

Query: 241 PLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF 300
            +A+  A+ IA  V  ALGG G+FGVELFV GD+V F E+SPRPHDTG+VTL+SQDLSEF
Sbjct: 241 SVAMAEARRIALAVTDALGGRGIFGVELFVKGDQVWFCEISPRPHDTGLVTLVSQDLSEF 300

Query: 301 ALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFGKPEID 359
           ALH RA LGLP+  IRQ GPAASAVIL +  S  V+F N+ + +   D  +RLFGKP + 
Sbjct: 301 ALHARAILGLPIPVIRQLGPAASAVILVEGESTEVSFGNLTDVLAEPDTALRLFGKPGVS 360

Query: 360 GSRRLGVALATAESVVDAIERAKHAAGQVKVQ 391
           G RR+GVALA   S+  A ++A  AA  VKV+
Sbjct: 361 GQRRMGVALARDVSIDAARQKALRAAAAVKVE 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: 471
Number of extensions: 17
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