GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Escherichia coli BW25113

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 16479 b2374 formyl-coenzyme A transferase (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__Keio:16479
          Length = 416

 Score =  191 bits (486), Expect = 3e-53
 Identities = 132/421 (31%), Positives = 205/421 (48%), Gaps = 35/421 (8%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  ++VLD + V +GP   Q+LA  GADVIK+ERPG GD TR          R     +A
Sbjct: 5   LQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTR-------HQLRDIPDIDA 57

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            Y+   N NK+S+ ++    EG+ ++ +L  ++DIL+ENF  G +   G  ++ ++ INP
Sbjct: 58  LYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINP 117

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +LI+ SI GF +  PY     Y+ + Q  GG  S TG  +G     P+    AL D  TG
Sbjct: 118 RLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGP----PLVSAAALGDSNTG 173

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDV-----QVACLANQAMNYL------------ 226
           ++    +LAAL HR+  G GQ + M++ D      +V     Q ++ L            
Sbjct: 174 MHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNG 233

Query: 227 TTGNAPKRLGNAHPN-----IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDP 281
           T G+A  R GNA        I+  + + T    +I     +  +    +  G+P+W  DP
Sbjct: 234 TFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDP 293

Query: 282 RFATNKVRVANRAVLIPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQAR 341
            ++T   R  +   +   I + TV     E V  L Q  +PC P+  + ++  DP ++  
Sbjct: 294 AYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQS 353

Query: 342 GLAMELPHLLAGKVPQVASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFR 401
           G  +E+   L GK   V  P++ S    + + A PLLGEHT  VLQ  LG  +  + A +
Sbjct: 354 GSVVEVEQPLRGKYLTVGCPMKFSAFTPDIK-AAPLLGEHTAAVLQE-LGYSDDEIAAMK 411

Query: 402 E 402
           +
Sbjct: 412 Q 412


Lambda     K      H
   0.319    0.137    0.408 

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: 415
Number of extensions: 23
Number of successful extensions: 5
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: 406
Length of database: 416
Length adjustment: 31
Effective length of query: 375
Effective length of database: 385
Effective search space:   144375
Effective search space used:   144375
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 (21.7 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