GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Dyella japonica UNC79MFTsu3.2

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate N515DRAFT_0021 N515DRAFT_0021 2-methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0021
          Length = 381

 Score =  580 bits (1494), Expect = e-170
 Identities = 282/380 (74%), Positives = 322/380 (84%)

Query: 18  SEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHG 77
           SE   P+ KKSVALSGV AGNTALCTVGR+GNDLHYRGYDI D+A    FEE+A+LLVHG
Sbjct: 2   SEQVLPKAKKSVALSGVAAGNTALCTVGRSGNDLHYRGYDIHDLAAKGCFEEVAYLLVHG 61

Query: 78  KLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHN 137
            LP  +EL AY+AKLK LRGLPA VK+ALE +PA+ HPMDVMRTG SVLGTVLPEK+DHN
Sbjct: 62  VLPNWAELNAYRAKLKRLRGLPAPVKSALELLPAATHPMDVMRTGCSVLGTVLPEKDDHN 121

Query: 138 TPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWER 197
             GARDIADRLMAS GSMLLYWYH+SHNG+RIE ETDD+SI  HFLHLLHG+K S L   
Sbjct: 122 LTGARDIADRLMASFGSMLLYWYHFSHNGKRIETETDDESIAAHFLHLLHGKKASELHAH 181

Query: 198 AMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKR 257
           A+  SL LYAEHEFNASTF ARVIAGTGSDMYS+I+GAIGALRGPKHGGANEVA EI  R
Sbjct: 182 ALDKSLILYAEHEFNASTFAARVIAGTGSDMYSAITGAIGALRGPKHGGANEVAMEIIAR 241

Query: 258 YDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAE 317
           Y N  EA+ADI  RV  KE++IGFGHPVYT  DPRN++IKEV++KL  + G+  +F+++E
Sbjct: 242 YRNAAEAEADIRARVERKEIIIGFGHPVYTVSDPRNEIIKEVSRKLCTEGGNPTLFEVSE 301

Query: 318 RLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKII 377
           R+E +MW++KKMFPNLDWFSA +YHMMGVPTAMFTPLFVIARTSGW+AH+IEQR D KII
Sbjct: 302 RIEKLMWELKKMFPNLDWFSASAYHMMGVPTAMFTPLFVIARTSGWSAHVIEQRQDGKII 361

Query: 378 RPSANYTGPENLKFVPIGKR 397
           RPSANYTGPE+  +VPI KR
Sbjct: 362 RPSANYTGPEDQAYVPIEKR 381


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: 547
Number of extensions: 10
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: 381
Length adjustment: 30
Effective length of query: 368
Effective length of database: 351
Effective search space:   129168
Effective search space used:   129168
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:

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