GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Desulfacinum infernum DSM 9756

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_073037622.1 BUB04_RS05220 CaiB/BaiF CoA-transferase family protein

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



>NCBI__GCF_900129305.1:WP_073037622.1
          Length = 400

 Score =  453 bits (1165), Expect = e-132
 Identities = 232/404 (57%), Positives = 287/404 (71%), Gaps = 12/404 (2%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           LS ++VLDLSRVLAGP+   +L D+GADVIKVERPG GDDTR WGPP       E   EA
Sbjct: 7   LSDVKVLDLSRVLAGPYCSMMLGDMGADVIKVERPGAGDDTRHWGPP-------EAGGEA 59

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
           AYYL  NRNK+S+T+D  + EG+ ++R LAA+SDILIEN+KVG L   GL Y  LK +NP
Sbjct: 60  AYYLCVNRNKRSITVDLKKEEGREIIRRLAAQSDILIENYKVGTLPKMGLGYVDLKKLNP 119

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +LIYCSITGFGQ GPY  + GYDFMIQG+GG+MS+TG P+G     P+KVGVA+ DI  G
Sbjct: 120 RLIYCSITGFGQNGPYKDKPGYDFMIQGMGGVMSITGDPDGP----PMKVGVAIVDITAG 175

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           L++ +AILAAL HRD  G GQ+ID+ALLD  VA LAN   NYL +G  P+R GNAHPNIV
Sbjct: 176 LFACSAILAALRHRDRTGRGQYIDIALLDAVVAWLANVGSNYLVSGELPRRYGNAHPNIV 235

Query: 244 PYQDFPTADGDFI-LTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302
           PY+ F T DG +I L VGND Q++ F  +AG    A DPRFATN  RV +R  LIPL+ +
Sbjct: 236 PYEPFKTRDGTYIALAVGNDRQWQDFCRLAGLDHLAHDPRFATNPQRVIHRDELIPLVAE 295

Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362
           A + KT  +W+ +L++  +PCGPIN L +VF+DPQV+AR +  E+PH  AG V  VASP+
Sbjct: 296 AMLKKTADQWLEELDKLKIPCGPINTLDRVFSDPQVKAREMVAEVPHPTAGSVKLVASPM 355

Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           + SETP      PPLLGEHT EVL   LG  +  +   RE GV+
Sbjct: 356 KFSETPCGIDRHPPLLGEHTDEVLHAELGYGDEEIARLRELGVV 399


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: 579
Number of extensions: 25
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: 406
Length of database: 400
Length adjustment: 31
Effective length of query: 375
Effective length of database: 369
Effective search space:   138375
Effective search space used:   138375
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 Apr 09 2024. 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