Alignments for a candidate for gcdG in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcdG in Azospirillum brasilense Sp245

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AZOBR_RS29180 AZOBR_RS29180 CoA-transferase

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



>FitnessBrowser__azobra:AZOBR_RS29180
          Length = 413

 Score =  457 bits (1177), Expect = e-133
 Identities = 235/406 (57%), Positives = 281/406 (69%), Gaps = 2/406 (0%)

Query: 3   ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62
           +L+ LRVLDLSRVLAGPWA QIL DLGAD+IK+E P  GDDTR+WGPP L+   G+ T +
Sbjct: 2   SLAGLRVLDLSRVLAGPWASQILGDLGADIIKIEHPEKGDDTRSWGPPNLRPTPGDRTDD 61

Query: 63  --AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
             +AYYLS NRNK+S+ ID  +PEG  LVR LA   D+++ENFKVGGL+ YGLDY+SLK 
Sbjct: 62  PPSAYYLSCNRNKRSLAIDIAKPEGAALVRRLARSCDVVLENFKVGGLSRYGLDYESLKR 121

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
            NP L+YCSITGFGQTGPYA R GYDF+IQG+ GLMS+TG+PEG  G+ P+KVGV ++D+
Sbjct: 122 ENPALVYCSITGFGQTGPYAPRGGYDFLIQGMSGLMSVTGQPEGAPGSEPLKVGVPVSDL 181

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
            TGLY+T A+LAAL HRD  G GQHID ALLD QVA LANQ MN+L  G  PKRLGN HP
Sbjct: 182 FTGLYATIAVLAALRHRDRAGEGQHIDCALLDTQVAVLANQGMNWLVGGQVPKRLGNGHP 241

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
           N+VPY+ F TADG  I+ VGNDGQFR    +  +     D RFA+N  R A+RA L   +
Sbjct: 242 NVVPYRCFATADGHIIVAVGNDGQFRALCRLLNREDLLADERFASNPGRQAHRAELEATL 301

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
             +    T+A+ +  L   GVP GPIN + QVF DPQV ARGL   L       VP V  
Sbjct: 302 ADSMARWTSADLIEALSGGGVPAGPINRIDQVFDDPQVVARGLVHRLETPGGTPVPIVGF 361

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           P RLS TP  YR  PP LGE T EVL  +L L    +   R  GV+
Sbjct: 362 PARLSRTPACYRRVPPRLGEQTDEVLSDLLDLTGNELEELRAGGVI 407


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: 604
Number of extensions: 21
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: 406
Length of database: 413
Length adjustment: 31
Effective length of query: 375
Effective length of database: 382
Effective search space:   143250
Effective search space used:   143250
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources