GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Brevibacterium jeotgali SJ5-8

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_101589879.1 BJEO58_RS12875 citrate synthase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>NCBI__GCF_900169175.1:WP_101589879.1
          Length = 428

 Score =  206 bits (524), Expect = 1e-57
 Identities = 127/386 (32%), Positives = 208/386 (53%), Gaps = 23/386 (5%)

Query: 11  GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70
           G     +  +A++ +      L YRGYD+ DL   + F EV+YLL+YGELPT  QL  + 
Sbjct: 45  GFANTASLSSAITYIDGDEGILRYRGYDIADLTEKSTFVEVSYLLIYGELPTPEQLADFD 104

Query: 71  GKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQ----DFSQQHDKTDRL 126
           G+LR+   L + ++   +  P DAHPM ++ +  + +     +     D +Q    T RL
Sbjct: 105 GRLREHTLLHEDMRRFFQAFPYDAHPMPMVSSAIAAMSTFYQDSLSITDEAQIDISTARL 164

Query: 127 LAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSE------LHVKVMNVS 180
           LA  P I  + +R + +G  +    + + +  +FL +  G  PSE      L +K ++  
Sbjct: 165 LAKMPTIAAFAHRHA-EGVPVVFPDNNLGLVENFLRVNFG-FPSEDYEVDPLALKALDQL 222

Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240
            IL+A+HE N ST T R+  S+ ++L+  I+A I +L GPLHGGAN A +EM+E   +  
Sbjct: 223 FILHADHEQNCSTSTVRLVGSSQANLYQSISAGIHALAGPLHGGANSAVLEMLEEIQASD 282

Query: 241 EAIEGTLGMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPVSE 295
           +  +  +  +  K+   ++MGFGH +YK+ DPR  +IK  + ++ +++G  D +L    +
Sbjct: 283 DGPKKFMERVKNKEDGVRLMGFGHRVYKNYDPRATIIKKTADEVLEKLGGNDEMLQLAKD 342

Query: 296 ----AIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE--QR 349
               A+    + ++KL+PN DFY    Y  +G PT +FT +F   RL GW A   E  + 
Sbjct: 343 LEEIALADDYFVERKLYPNVDFYTGLIYKALGFPTNMFTVLFAVGRLPGWIAQWREAAKD 402

Query: 350 ANNRIIRPSAEYTGVEQRKFVPIEQR 375
           +  +I RP   YTG  +R + P++ R
Sbjct: 403 SETKIGRPRQIYTGAPKRLYTPVDDR 428


Lambda     K      H
   0.321    0.135    0.406 

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: 370
Number of extensions: 21
Number of successful extensions: 5
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: 375
Length of database: 428
Length adjustment: 31
Effective length of query: 344
Effective length of database: 397
Effective search space:   136568
Effective search space used:   136568
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 (21.9 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