GapMind for catabolism of small carbon sources

 

Alignments for a candidate for antC in Klebsiella michiganensis M5al

Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate BWI76_RS13715 BWI76_RS13715 2-chlorobenzoate 1 2-dioxygenase electron transfer subunit

Query= reanno::WCS417:GFF4631
         (335 letters)



>FitnessBrowser__Koxy:BWI76_RS13715
          Length = 338

 Score =  249 bits (635), Expect = 9e-71
 Identities = 142/339 (41%), Positives = 203/339 (59%), Gaps = 12/339 (3%)

Query: 1   MNHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYS-- 58
           M   +A +F DG T F    A E +LDAA R  + +P+DC +GVCGTC+ RC SG+Y   
Sbjct: 1   MTFNIALNFEDGITRFIQCHAGEKVLDAAYRQQVNLPMDCSDGVCGTCKCRCVSGEYGLG 60

Query: 59  QDYVDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVS 118
            D++ EEALS  +  +R++L+CQ    SD        ++ C       +    +AV+QV+
Sbjct: 61  DDFL-EEALSEDEAAERQVLTCQMVPTSDCVIDVPAAAAQCKTA----LASLGAAVKQVN 115

Query: 119 --ASTAI-LQVQLDQALDFLPGQYARLSVPGTDSWRSYSFANLPGNHL-QFLVRLLPDGV 174
             + TAI L V LD+ LDFLPGQY  + VPGT   R+YSF++LPG+    FL+R +P G+
Sbjct: 116 LLSDTAIELVVVLDEPLDFLPGQYINIEVPGTPQARAYSFSSLPGSREGSFLIRNVPGGL 175

Query: 175 MSNYLRERCQVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQP 234
           MS +L +R   GD L +  P+G+FYLR   +PL+L+AGGTGL+ LL ML  L      +P
Sbjct: 176 MSQWLTQRASPGDRLTLSGPMGSFYLRGGERPLLLLAGGTGLAPLLSMLQTLVMQRSTRP 235

Query: 235 VHLYYGVRGAEDLCEAARIRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAELRD 294
           V L YGV    DL +   + A+  ++P  R+  V+ A ++    +RG++TEH D A L D
Sbjct: 236 VTLLYGVTRDCDLVKTDALEAFTGQLPAYRWLPVV-ADAQSGCPQRGFVTEHLDDAILND 294

Query: 295 GSADMYLCGPPPMVESIQQWLADQALDGVQLYYEKFTQS 333
           G  D+YLCGPPPMV ++   L ++ +     +YEKF  S
Sbjct: 295 GDVDIYLCGPPPMVNAVATALRERGVSPAGFWYEKFIAS 333


Lambda     K      H
   0.320    0.136    0.412 

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: 323
Number of extensions: 13
Number of successful extensions: 5
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: 335
Length of database: 338
Length adjustment: 28
Effective length of query: 307
Effective length of database: 310
Effective search space:    95170
Effective search space used:    95170
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: 49 (23.5 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