GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpC in Azospirillum brasilense Sp245

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate AZOBR_RS24300 AZOBR_RS24300 methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS24300 AZOBR_RS24300
           methylcitrate synthase
          Length = 387

 Score =  655 bits (1690), Expect = 0.0
 Identities = 322/388 (82%), Positives = 348/388 (89%), Gaps = 2/388 (0%)

Query: 11  AAPDATASEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEI 70
           +AP+  A  P  P  KKSVALSGVTAGNTALCTVG++GNDLHYRGYDILDIAE CEFEE+
Sbjct: 2   SAPETAAPTPFKP--KKSVALSGVTAGNTALCTVGKSGNDLHYRGYDILDIAERCEFEEV 59

Query: 71  AHLLVHGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVL 130
           A+LLVHGKLPT +EL AYKAKL+SLRGLP NV+ ALE +PASAHPMDVMRTGVS LG  L
Sbjct: 60  AYLLVHGKLPTFAELKAYKAKLQSLRGLPTNVRQALECLPASAHPMDVMRTGVSALGCAL 119

Query: 131 PEKEDHNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEK 190
           PEK+DHN PGARDIADRLMASLGSMLLYWYH+S NGRRIEVETDD+SIG HFLHLLHG K
Sbjct: 120 PEKDDHNIPGARDIADRLMASLGSMLLYWYHWSSNGRRIEVETDDESIGAHFLHLLHGRK 179

Query: 191 PSALWERAMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEV 250
           PSALWERAMHTSL LYAEHEFNASTFT RVIAGTGSD+YS+I+GAIGALRGPKHGGANEV
Sbjct: 180 PSALWERAMHTSLILYAEHEFNASTFTGRVIAGTGSDLYSAITGAIGALRGPKHGGANEV 239

Query: 251 AFEIQKRYDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSM 310
           AFEIQKRYD PDEA+ADI RRV NKEVVIGFGHPVYT  DPRN VI+ VA KLS DAGS 
Sbjct: 240 AFEIQKRYDTPDEAEADIRRRVENKEVVIGFGHPVYTVSDPRNDVIRGVAHKLSVDAGSA 299

Query: 311 KMFDIAERLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQ 370
           +MFDIA RLE VMW++K+MFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQ
Sbjct: 300 RMFDIAARLEAVMWEVKRMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQ 359

Query: 371 RIDNKIIRPSANYTGPENLKFVPIGKRK 398
           RIDNKIIRPSANY GP++  FV I +R+
Sbjct: 360 RIDNKIIRPSANYVGPDDRVFVAIDQRQ 387


Lambda     K      H
   0.317    0.133    0.396 

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: 588
Number of extensions: 13
Number of successful extensions: 1
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: 398
Length of database: 387
Length adjustment: 31
Effective length of query: 367
Effective length of database: 356
Effective search space:   130652
Effective search space used:   130652
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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