Aligments for a candidate for uxaA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_2834 PP_2834 Putative D-galactarate
           dehydratase/Altronate dehydratase
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources