GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Halomonas xinjiangensis TRM 0175

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_043530514.1 JH15_RS12215 2-methylcitrate synthase

Query= SwissProt::Q8EJW2
         (375 letters)



>NCBI__GCF_000759345.1:WP_043530514.1
          Length = 375

 Score =  575 bits (1482), Expect = e-169
 Identities = 278/371 (74%), Positives = 309/371 (83%)

Query: 5   KKLTGAGLRGQSAGETALSTVGVSGSGLTYRGYDVKDLAENATFEEVAYLILYGELPTTA 64
           K     GLRGQSAG TAL TVG SGSGLTYRGYD+ DLAE+A FEEVAYL+L G+LP  +
Sbjct: 4   KTPASTGLRGQSAGSTALCTVGKSGSGLTYRGYDIHDLAEHARFEEVAYLLLKGKLPNAS 63

Query: 65  QLAAYKTKLKGMRGLPQALKEVLERIPADAHPMDVMRTGCSMLGNLEAEHSFSEQSQIAD 124
           +L  Y  KLKG+R LP+ LK VLE+IP +AHPMDVMRTG SMLGNLE E  F  Q   +D
Sbjct: 64  ELQNYVDKLKGLRSLPEPLKAVLEQIPREAHPMDVMRTGASMLGNLETEGDFEAQQDASD 123

Query: 125 RLLAAFPSIICYWYRFSHDGVRIDTETDDDQIGAHFLHLLHGKAPSALHTKVMDVSLILY 184
           RLLA  PSIICYWYR++HDGVRIDT+TDDD +GAHFLHLL G+APS LH +VM+VSLILY
Sbjct: 124 RLLAVLPSIICYWYRYTHDGVRIDTDTDDDSVGAHFLHLLRGEAPSELHARVMNVSLILY 183

Query: 185 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMKDEADARD 244
           AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAM +I+D +   +A  
Sbjct: 184 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMAMIEDWQTPDEAER 243

Query: 245 VLMGKLERKEKIMGFGHAIYRDSDPRNAIIKEWSEKLAADYGDDRLYRVSVACEALMWEQ 304
            +MG LER+EKIMGFGHAIYRDSDPRNAIIK+WS++LA D GDDRLY VSV CE +MW +
Sbjct: 244 EIMGMLERREKIMGFGHAIYRDSDPRNAIIKQWSKRLADDVGDDRLYPVSVRCEEVMWRE 303

Query: 305 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWTAHVMEQRSNNRIIRPSADYVGV 364
           KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGW AHV EQR NNRIIRPSADY+G 
Sbjct: 304 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWCAHVFEQRENNRIIRPSADYIGP 363

Query: 365 SPRKVIPIANR 375
                +PI  R
Sbjct: 364 EKTDWVPIEQR 374


Lambda     K      H
   0.320    0.134    0.401 

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: 519
Number of extensions: 8
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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