GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpC in Synechococcus elongatus PCC 7942

Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate Synpcc7942_0612 Synpcc7942_0612 methylcitrate synthase

Query= BRENDA::P45858
         (372 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0612 Synpcc7942_0612
           methylcitrate synthase
          Length = 386

 Score =  243 bits (619), Expect = 8e-69
 Identities = 143/370 (38%), Positives = 207/370 (55%), Gaps = 8/370 (2%)

Query: 1   MEEKQHYSPGLDGVIAAETHISYLDTQSSQILIRGYDLIELSETKSYLELVHLLLEGRLP 60
           M     + PGL+GV A  + IS++D Q   +  RG  + +L++  S+LE  +LL+ G LP
Sbjct: 1   MTAVSEFRPGLEGVPATLSSISFVDGQRGVLEYRGISIEQLAQQSSFLETAYLLIWGHLP 60

Query: 61  EESEMETLERKINSASSLPADHLRLLELLPEDTHPMDGLRTGLSALAGY--DRQIDDRSP 118
            + E+   E +I     +      +++  P+  HPMD L+   +AL  +   R +DD  P
Sbjct: 61  TQQELTEFEHEIRYHRRIKFRIRDMMKCFPDSGHPMDALQASAAALGLFYSRRALDD--P 118

Query: 119 SANKERAYQLLGKMPALTAASYRIINKKEPILPLQTLSYSANFLYMMTGKLPSSLEEQIF 178
              +    +LL K+P + AA   I    +PI P   L Y+ANFLYM+T + P  +  +IF
Sbjct: 119 EYIRAAVVRLLAKIPTMVAAFQLIRKGNDPIQPRDELDYAANFLYMLTEREPDPVAARIF 178

Query: 179 DRSLVLYSEHEMPNSTFAARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAK 238
           D  L L++EH +  STF+A V AST +D Y  +  AV +L G LHGGANE V+ +L    
Sbjct: 179 DICLTLHAEHTINASTFSAMVTASTLTDPYAVVASAVGTLAGPLHGGANEEVLDMLEAIG 238

Query: 239 TTSDFEQLLQTKLKRKEKIMGFGHRVYMKKMDPRALMMKEALQQLCDKAGDHRLYEMCEA 298
           +  + E  L   +  K +IMGFGHRVY K  DPRA++++   +QL D  G    YE+  A
Sbjct: 239 SVENVEPYLDHCIATKTRIMGFGHRVY-KVKDPRAVILQNLAEQLFDIFGHDPYYEIAVA 297

Query: 299 GERLMEK---EKGLYPNLDYYAAPVYWMLGIPIPLYTPIFFSARTSGLCAHVIEQHANNR 355
            E+   +    KG+YPN+D+Y+  VY  LGIP  L+TP+F  AR +G  AH  EQ   NR
Sbjct: 298 VEKAAAERLSHKGIYPNVDFYSGLVYRKLGIPSDLFTPVFAIARVAGWLAHWKEQLNENR 357

Query: 356 LFRPRVSYMG 365
           +FRP   Y G
Sbjct: 358 IFRPTQIYTG 367


Lambda     K      H
   0.317    0.134    0.381 

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: 341
Number of extensions: 13
Number of successful extensions: 4
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: 372
Length of database: 386
Length adjustment: 30
Effective length of query: 342
Effective length of database: 356
Effective search space:   121752
Effective search space used:   121752
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