GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas simiae WCS417

Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate GFF4111 PS417_21060 2-methylcitrate dehydratase

Query= SwissProt::Q937N6
         (484 letters)



>FitnessBrowser__WCS417:GFF4111
          Length = 494

 Score =  594 bits (1531), Expect = e-174
 Identities = 305/497 (61%), Positives = 366/497 (73%), Gaps = 16/497 (3%)

Query: 1   MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60
           MS +     RPD DQ+L DI DYV  Y I S  A DTARNCL+DTLGCGL AL +P CTK
Sbjct: 1   MSANVDQNNRPDYDQLLQDIADYVLNYRIDSRDALDTARNCLMDTLGCGLLALRFPECTK 60

Query: 61  LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120
            LGP+V GT+VP GARVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGG
Sbjct: 61  HLGPIVEGTVVPFGARVPGTSFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGG 120

Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180
           ILA AD +S+  +A G  PLT++AVL AMI AHEIQG IALENSFN+VGLDHV+LVKVAS
Sbjct: 121 ILAVADHLSQKRVANGDVPLTVRAVLEAMIMAHEIQGVIALENSFNRVGLDHVLLVKVAS 180

Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240
           TAV A+++G  R+++L A+S A+VDGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA IA
Sbjct: 181 TAVTAKLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIA 240

Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK------------GQPFRFQRPYGTYVMENILLKISY 288
             GEMG P VL+A  WGFYDVLF              + F   +PYGTYVMEN+L KIS+
Sbjct: 241 MRGEMGIPGVLSAPQWGFYDVLFSHTNKDLALKPEDRRAFSLSQPYGTYVMENVLFKISF 300

Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348
           PAEFHAQTA EAA+ LH           +I  I I THE+ +RII K+G L+N ADRDHC
Sbjct: 301 PAEFHAQTACEAAVTLH---PWVKDRLHEIDRIVITTHESAIRIISKVGQLANAADRDHC 357

Query: 349 IQYMVAVPLLFGRLTAADYEDRI-AADPRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407
           +QYM AVPL FG L A  YED   AA P ID LR ++  VEDP  +R+Y +  KRSIANA
Sbjct: 358 LQYMTAVPLAFGNLVAEQYEDEFHAAHPIIDQLRDKMVIVEDPRYSREYLEADKRSIANA 417

Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467
           + V   DG+  ++V VEYP+GH+RRR EGIPLL +KF+ NLA RF  ++   I A   DQ
Sbjct: 418 VQVFFKDGSCTEQVAVEYPIGHRRRRVEGIPLLEDKFKANLATRFTGQRSAEIFALCKDQ 477

Query: 468 ARLEAMPVNEYLDMYAI 484
           ARLEA PVN ++D++ I
Sbjct: 478 ARLEATPVNRFVDLFVI 494


Lambda     K      H
   0.322    0.136    0.410 

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: 666
Number of extensions: 25
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: 484
Length of database: 494
Length adjustment: 34
Effective length of query: 450
Effective length of database: 460
Effective search space:   207000
Effective search space used:   207000
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:

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