GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Shewanella halifaxensis HAW-EB4

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_012277058.1 SHAL_RS10215 2-methylcitrate synthase

Query= SwissProt::Q8EJW2
         (375 letters)



>NCBI__GCF_000019185.1:WP_012277058.1
          Length = 379

 Score =  590 bits (1521), Expect = e-173
 Identities = 285/372 (76%), Positives = 318/372 (85%)

Query: 4   AKKLTGAGLRGQSAGETALSTVGVSGSGLTYRGYDVKDLAENATFEEVAYLILYGELPTT 63
           +KK+ GAGLRGQSAGETAL TVG SGSGLTY GYDV DLA+NATFEEVAYL+  GELP  
Sbjct: 8   SKKIGGAGLRGQSAGETALCTVGKSGSGLTYCGYDVSDLADNATFEEVAYLLFNGELPNQ 67

Query: 64  AQLAAYKTKLKGMRGLPQALKEVLERIPADAHPMDVMRTGCSMLGNLEAEHSFSEQSQIA 123
            QL  YKT+L   R LPQALKEVL+RIPA+AHPMDVMRTGCS LGNLE E+ FSEQ++ A
Sbjct: 68  TQLDHYKTELFAHRDLPQALKEVLQRIPAEAHPMDVMRTGCSFLGNLEPENDFSEQNRAA 127

Query: 124 DRLLAAFPSIICYWYRFSHDGVRIDTETDDDQIGAHFLHLLHGKAPSALHTKVMDVSLIL 183
           +RLLAAFP+I+CYWY+FSH+GV ID  TD+D IG HFLHLL+GKAPS  H +VMDVSLIL
Sbjct: 128 NRLLAAFPAIMCYWYKFSHEGVEIDCVTDEDSIGGHFLHLLNGKAPSEQHRRVMDVSLIL 187

Query: 184 YAEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMKDEADAR 243
           YAEHEFNASTFTARVCASTLSDM+SC+TGAIG+LRGPLHGGANEAAM++IQ      DA+
Sbjct: 188 YAEHEFNASTFTARVCASTLSDMYSCITGAIGTLRGPLHGGANEAAMDMIQKFSSPEDAK 247

Query: 244 DVLMGKLERKEKIMGFGHAIYRDSDPRNAIIKEWSEKLAADYGDDRLYRVSVACEALMWE 303
           + + G LERKEKIMGFGHAIYR SDPRN IIK WS+KL A++GD  LY +SVACE  MW+
Sbjct: 248 EQMAGMLERKEKIMGFGHAIYRTSDPRNVIIKAWSKKLGAEFGDSSLYDISVACEEFMWD 307

Query: 304 QKKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWTAHVMEQRSNNRIIRPSADYVG 363
            KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSR+TGW AHVMEQRSNNRIIRPSADY G
Sbjct: 308 TKKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVMEQRSNNRIIRPSADYTG 367

Query: 364 VSPRKVIPIANR 375
             PR V PI+ R
Sbjct: 368 SEPRTVTPISER 379


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: 494
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: 375
Length of database: 379
Length adjustment: 30
Effective length of query: 345
Effective length of database: 349
Effective search space:   120405
Effective search space used:   120405
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.

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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