GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_3309 Ga0059261_3309 formate-dependent phosphoribosylglycinamide formyltransferase (EC 6.3.4.-)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__Korea:Ga0059261_3309
          Length = 388

 Score =  401 bits (1030), Expect = e-116
 Identities = 212/380 (55%), Positives = 263/380 (69%), Gaps = 3/380 (0%)

Query: 14  RVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVEL 73
           +++LLGSGELG+E  I  +RLG +VIA D YA+APAM VA    V +MLDG+ALR  +  
Sbjct: 6   KILLLGSGELGREFVISAKRLGAQVIACDSYANAPAMQVADGHEVFSMLDGEALRAAIAK 65

Query: 74  EKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYR 133
             P Y+VPE+EAI T++L  +E EG+ VVP ARA ++TMNR+GIR +AA EL L TS YR
Sbjct: 66  HAPDYVVPEVEAIRTEVLADVEAEGVTVVPSARAAQMTMNRDGIREVAAVELGLRTSRYR 125

Query: 134 FADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVI 193
           +A+S           G PC++KPVMSSSGKGQ+ +R A  L  AW YA    R    RVI
Sbjct: 126 YAESLEEVLAGAEHTGLPCVIKPVMSSSGKGQSTVREASALEAAWDYAVANMRGDRARVI 185

Query: 194 VEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARK 253
           VE  V FD+EITLLTV +  GV FC P+GHRQE GDY+ESWQP  MS  A+  AQ++ARK
Sbjct: 186 VEEFVDFDYEITLLTVRSRAGVSFCPPIGHRQERGDYQESWQPAAMSAQAIADAQDMARK 245

Query: 254 VVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVG 313
           VV  LGGYG+FGVE FV G+EVIFSE+SPRPHDTGMVTLISQ+LSEF LH RA LGLPV 
Sbjct: 246 VVDDLGGYGIFGVEFFVKGEEVIFSELSPRPHDTGMVTLISQNLSEFDLHARAVLGLPVP 305

Query: 314 GIRQYGPAASAVILPQLTSQNVTFDNVQNAV---GADLQIRLFGKPEIDGSRRLGVALAT 370
            +R YGP+ASAVIL     +   ++ V  A+   G ++ +R+F KP     RR+GVALA 
Sbjct: 306 EVRLYGPSASAVILADRDGEAPGYEGVAEALAVPGGEIDLRIFAKPTTRPYRRMGVALAL 365

Query: 371 AESVVDAIERAKHAAGQVKV 390
           A     A   A  AAG+V++
Sbjct: 366 AGDTGAARTLAAEAAGKVRI 385


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: 442
Number of extensions: 16
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: 388
Length adjustment: 31
Effective length of query: 361
Effective length of database: 357
Effective search space:   128877
Effective search space used:   128877
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