GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:16479 b2374 formyl-coenzyme A transferase
           (NCBI)
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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