GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate AO353_00880 AO353_00880 2-methylcitrate dehydratase

Query= BRENDA::P74840
         (483 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 AO353_00880
           2-methylcitrate dehydratase
          Length = 494

 Score =  600 bits (1547), Expect = e-176
 Identities = 306/492 (62%), Positives = 370/492 (75%), Gaps = 16/492 (3%)

Query: 5   ELNIRPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPI 64
           +LNIRPD+D+ + DI DYV+N++I SK A DTA  CL+DTLGCGL AL +P C K LGPI
Sbjct: 6   DLNIRPDYDKVLQDIADYVLNFKIESKEALDTARNCLMDTLGCGLLALRFPECTKHLGPI 65

Query: 65  VPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATA 124
           V GTVVP GARVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGGILA A
Sbjct: 66  VEGTVVPFGARVPGTHFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVA 125

Query: 125 DWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVASTAVVA 184
           D LS+  VA G APLTM+ VL  MI AHEIQG IALEN+FNRVGLDHVLLVKVASTAV A
Sbjct: 126 DHLSQKRVANGDAPLTMRAVLDAMIMAHEIQGVIALENSFNRVGLDHVLLVKVASTAVTA 185

Query: 185 EMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEM 244
           +++G  R+++L A+S A+VDGQ+LRTYRHAPN G+RKSWAAGDA+SR VRLA +A  GEM
Sbjct: 186 KLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEM 245

Query: 245 GYPSALTAKTWGFYDVSFK------------GETFRFQRPYGSYVMENVLFKISFPAEFH 292
           G P  LTA  WGFYDV F               TF   + YG+YVMENVLFKISFPAEFH
Sbjct: 246 GIPGVLTAPQWGFYDVLFSHTNKDLALKPADKRTFSLSQKYGTYVMENVLFKISFPAEFH 305

Query: 293 SQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMV 352
           +QTA EAA+TL+ Q+        +I+K+ I THE+ +RII K G L N ADRDHCIQYM 
Sbjct: 306 AQTACEAAVTLHPQV---SNRLDEIDKIVITTHESAIRIISKVGQLANAADRDHCIQYMT 362

Query: 353 AVPLLFGRLTAADYEDEV-AQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEF 411
           AVPL FG L A  YED+  A    ID LR+K+V  EDP +T +Y + +KR+I NA+ V F
Sbjct: 363 AVPLAFGTLVAEQYEDQFHAAHPIIDELRKKMVIVEDPRYTREYLEADKRSIANALQVFF 422

Query: 412 TDGSRFGEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQ 471
            DGS  G+VVVEYPIGH RRRA+GIP L +KFK NLA +F  ++  +I  +  D+A+LE 
Sbjct: 423 KDGSSTGQVVVEYPIGHRRRRAEGIPLLEDKFKANLATRFTAQRSAQIFALCQDQAKLEA 482

Query: 472 MPVNEYLDLYVI 483
            PVN ++DL+VI
Sbjct: 483 TPVNRFMDLFVI 494


Lambda     K      H
   0.321    0.136    0.408 

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: 658
Number of extensions: 20
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
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: 52 (24.6 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 preprint 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