GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaA in Pseudomonas putida KT2440

Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate PP_2834 PP_2834 Putative D-galactarate dehydratase/Altronate dehydratase

Query= SwissProt::P42604
         (495 letters)



>FitnessBrowser__Putida:PP_2834
          Length = 513

 Score =  283 bits (725), Expect = 8e-81
 Identities = 176/492 (35%), Positives = 264/492 (53%), Gaps = 17/492 (3%)

Query: 4   IKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIG 63
           I+++ LDNV +A   L  G  V +D + +T+RQ +  GHK A   +A+G  + +YG  IG
Sbjct: 13  IRLNPLDNVVIARQALLPG--VRLDAEAITVRQPIPSGHKLATEPVAQGQPLRRYGQIIG 70

Query: 64  YALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADREVQIYRRANGDVGVRNE 123
           +A   I AG HVH HN +      D Y +  D + LP  AA  + Q   RA+G V  RN 
Sbjct: 71  FASQAIDAGDHVHVHNVQMGDFARD-YAFGVDTRSLPGSAA--QFQGIVRADGRVATRNY 127

Query: 124 LWILPTVGCVNGIARQIQNRFLKETN-----NAEGTDGVFLFSHTYGCS--QLGDDHINT 176
           + IL +V C   +AR + + F ++ +     +    DGV   SH+ GC+    G+     
Sbjct: 128 IGILTSVNCSATVARAVADHFRRDIHPEVLADYPNVDGVVALSHSAGCAVDPSGEALGLL 187

Query: 177 RTMLQNMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQ---QDDEIEA 233
           R  L     HPN  AVL+IGLGCE NQ+    ET G     ++     Q        I A
Sbjct: 188 RRTLAGYAVHPNFAAVLIIGLGCETNQIETLLETQGLQASAQLRAFTIQGIGGTSKTIAA 247

Query: 234 GIEHLHQLYNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTT 293
           GI  +  L       +R+P     L  GL+CGGSDG SGITANP LG   D ++A GGT 
Sbjct: 248 GIAQVKALLAEANQVRRQPVSARHLVVGLQCGGSDGYSGITANPALGNAVDRLVAAGGTA 307

Query: 294 VLTEVPEMFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGIT 353
           +L+E PE++GAE LL          EKLV  +  ++ Y    +  +  NPS GNKAGG+T
Sbjct: 308 ILSETPEIYGAEHLLTRRAVSREVGEKLVARIRWWEDYCQRMNAELNNNPSAGNKAGGLT 367

Query: 354 TLEDKSLGCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFS 413
           T+ +KSLG   KAGSS +VDV +Y + ++  GL  +  PG D V+ +     G +++ F+
Sbjct: 368 TILEKSLGAVAKAGSSNLVDVYQYAQAVRAQGLVFMDTPGYDPVSATGQVAGGANLIAFT 427

Query: 414 TGRGTPYG-GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKAMPQLLEEFI-DTIVEFA 471
           TGRG+ YG    P++K+ATN+ +   ++  +D + G +  G    +    FI + ++  A
Sbjct: 428 TGRGSAYGCAPAPSIKLATNNRVFEHQQEDMDVNCGGIADGSTSIEERGAFIFEQMLRIA 487

Query: 472 NGKQTCNERNDF 483
           +G+++ +E++ +
Sbjct: 488 SGERSKSEQHGY 499


Lambda     K      H
   0.319    0.136    0.403 

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: 644
Number of extensions: 38
Number of successful extensions: 6
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: 495
Length of database: 513
Length adjustment: 34
Effective length of query: 461
Effective length of database: 479
Effective search space:   220819
Effective search space used:   220819
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 (21.7 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