GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Shewanella oneidensis MR-1

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 202710 SO3613 phosphoribosylglycinamide formyltransferase 2 (NCBI ptt file)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__MR1:202710
          Length = 378

 Score =  520 bits (1338), Expect = e-152
 Identities = 261/376 (69%), Positives = 310/376 (82%), Gaps = 1/376 (0%)

Query: 16  MLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEK 75
           MLLG GELGKEVAIE QRLGVEVI VDRY +APAM +AHRSHVINMLD  ALR V+ELEK
Sbjct: 1   MLLGCGELGKEVAIELQRLGVEVIGVDRYPNAPAMQIAHRSHVINMLDAKALRAVIELEK 60

Query: 76  PHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFA 135
           PH ++PEIEAIAT  L+++E EGLNVVP ARATKLTM+REGIRRLAAE L LPTS Y F 
Sbjct: 61  PHLVIPEIEAIATQTLVEMEAEGLNVVPTARATKLTMDREGIRRLAAETLGLPTSPYFFC 120

Query: 136 DSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVIVE 195
           D+E+ F +A++ IG PC+VKPVMSSSGKGQ+ IR+  Q A+AW+YAQ+GGRAG GRVIVE
Sbjct: 121 DTETEFNQAISKIGVPCVVKPVMSSSGKGQSVIRNVAQSAKAWQYAQEGGRAGGGRVIVE 180

Query: 196 GVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVV 255
           G + FD+EITLLT+SAV+G+HFCAP+GHRQEDGDYRESWQPQ MS   L ++Q IA KVV
Sbjct: 181 GFIPFDYEITLLTISAVNGIHFCAPIGHRQEDGDYRESWQPQAMSADVLAKSQAIASKVV 240

Query: 256 LALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGI 315
            ALGGYGLFGVELFV G +V FSEVSPRPHDTG+VTLISQDLSEFALHVRA LGLP+  I
Sbjct: 241 EALGGYGLFGVELFVKGSDVYFSEVSPRPHDTGLVTLISQDLSEFALHVRAILGLPIPNI 300

Query: 316 RQYGPAASAVILPQLTSQNVTFDNVQNAVGAD-LQIRLFGKPEIDGSRRLGVALATAESV 374
            Q+GP+ASAV+L +  S+N+ +  +  A+ A+  Q+RLF KPEIDG RRLGVALA  + +
Sbjct: 301 HQHGPSASAVVLVEGKSKNIRYQGLAAALAAENTQLRLFAKPEIDGRRRLGVALARDKDI 360

Query: 375 VDAIERAKHAAGQVKV 390
             A+ +A  +A +V+V
Sbjct: 361 DSAVNKALDSAAKVQV 376


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: 453
Number of extensions: 11
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: 378
Length adjustment: 30
Effective length of query: 362
Effective length of database: 348
Effective search space:   125976
Effective search space used:   125976
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