GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Flavobacterium glycines Gm-149

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 WP_066326848.1 BLR17_RS05725 formate-dependent phosphoribosylglycinamide formyltransferase

Query= SwissProt::P33221
         (392 letters)



>NCBI__GCF_900100165.1:WP_066326848.1
          Length = 387

 Score =  356 bits (913), Expect = e-103
 Identities = 196/375 (52%), Positives = 253/375 (67%), Gaps = 4/375 (1%)

Query: 14  RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73
           +++LLGSGELGKE  I  QR+G  VIAVD YA+APAM VAH   VINMLDG+ L ++V  
Sbjct: 3   KILLLGSGELGKEFVIAAQRIGQTVIAVDSYANAPAMQVAHDFEVINMLDGETLDKIVAK 62

Query: 74  EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133
            +P +IVPEIEAI T+     E++G+ VVP A+A   TMNR+ IR LA++EL L T+ YR
Sbjct: 63  HQPDFIVPEIEAIRTERFYDYEKQGITVVPSAKAANFTMNRKAIRDLASKELGLKTAEYR 122

Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193
           +A +    R+ V ++G PC+VKP+MSSSGKGQ+ I++   + +AW+YA  G R     VI
Sbjct: 123 YATTAEELRKGVLEVGIPCVVKPLMSSSGKGQSTIKTEADIDKAWEYAVAGSRGDVVEVI 182

Query: 194 VEGVVKFDFEITLLTVSAVD-GVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIAR 252
           VE  VKF+ EITLLTV+  +    FCAP+GHRQE GDY+ESWQP ++S   L  AQ++A 
Sbjct: 183 VEAFVKFNSEITLLTVTQNNRRTLFCAPIGHRQERGDYQESWQPARISDKDLYEAQDMAE 242

Query: 253 KVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLI-SQDLSEFALHVRAFLGLP 311
           KV  ALGG GLFGVE F+  D V FSE+SPRPHDTGMVTL  +Q+ +EF LH+RA L LP
Sbjct: 243 KVTEALGGAGLFGVEFFIADDGVYFSELSPRPHDTGMVTLAGTQNFNEFELHLRAILSLP 302

Query: 312 VGGIRQYGPAASAVILPQLTSQNVTFDNV-QNAVGADLQIRLFGKPEIDGSRRLGVALAT 370
           +  I      ASAVIL    S N T++ + Q A       R+FGKP     RR+GVAL T
Sbjct: 303 IFEITLEKAGASAVILASDNSTNPTYNGIEQIAALPKTDFRIFGKPSSRPYRRMGVAL-T 361

Query: 371 AESVVDAIERAKHAA 385
           ++S+   IE    +A
Sbjct: 362 SDSLETPIEEIVKSA 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: 357
Number of extensions: 10
Number of successful extensions: 4
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: 387
Length adjustment: 30
Effective length of query: 362
Effective length of database: 357
Effective search space:   129234
Effective search space used:   129234
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 24 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