GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Lysobacter daejeonensis GH1-9

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_036137781.1 N800_RS09910 2-methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>NCBI__GCF_000768355.1:WP_036137781.1
          Length = 383

 Score =  557 bits (1436), Expect = e-163
 Identities = 269/382 (70%), Positives = 314/382 (82%)

Query: 16  TASEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLV 75
           T S    P+ KKSVALSG  AGNTALCTVGR+GNDLHYRGYDI D+A    FEE+AHLLV
Sbjct: 2   TESAQVLPKAKKSVALSGTAAGNTALCTVGRSGNDLHYRGYDIHDLATKSSFEEVAHLLV 61

Query: 76  HGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKED 135
           HG LPT S+L AY+ KLK LRGLPA V  ALE VPA+AHPMDV+RTG SVLGTVLPE+E 
Sbjct: 62  HGALPTTSQLKAYRTKLKRLRGLPAIVAEALELVPANAHPMDVLRTGCSVLGTVLPEREG 121

Query: 136 HNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALW 195
           H    ARDIAD+L+AS GSMLLYW+H++ NGRRI+VETDD++   HFLHLLHGE PSAL 
Sbjct: 122 HPANEARDIADKLIASFGSMLLYWWHFTRNGRRIDVETDDETTAAHFLHLLHGEAPSALH 181

Query: 196 ERAMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQ 255
             ++  SL LYAEHEFNASTFTARVIAGTGSD++S I+GAIGALRGPKHGGANEVA +I 
Sbjct: 182 AESLDKSLVLYAEHEFNASTFTARVIAGTGSDLHSCITGAIGALRGPKHGGANEVAMDII 241

Query: 256 KRYDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDI 315
            RY + D A+ADI  R+  KE+VIGFGHPVYT GDPRN +IKE+++KL  D G+  +FD+
Sbjct: 242 SRYGDADAAEADIRARMERKEIVIGFGHPVYTIGDPRNPIIKEISRKLCADGGNQTLFDV 301

Query: 316 AERLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNK 375
           +ER+E +M D KKMFPNLDW+SA +YHMMG+PT MFTPLFVIART+GW+AH+IEQR D K
Sbjct: 302 SERIENLMMDTKKMFPNLDWYSASAYHMMGIPTPMFTPLFVIARTTGWSAHVIEQREDGK 361

Query: 376 IIRPSANYTGPENLKFVPIGKR 397
           IIRPSANYTGPE+  +VPI KR
Sbjct: 362 IIRPSANYTGPEDQAYVPIEKR 383


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: 518
Number of extensions: 9
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: 383
Length adjustment: 31
Effective length of query: 367
Effective length of database: 352
Effective search space:   129184
Effective search space used:   129184
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 24 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