Aligments for a candidate for xad in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for xad in Pseudomonas putida KT2440

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate PP_5128 PP_5128 Dihydroxy-acid dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1668
         (594 letters)



>FitnessBrowser__Putida:PP_5128
          Length = 613

 Score =  214 bits (546), Expect = 6e-60
 Identities = 172/563 (30%), Positives = 259/563 (46%), Gaps = 71/563 (12%)

Query: 35  GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94
           GM  E+ +  +PII IA + +   P + H  +L Q V   I  AGG+  EF    + +  
Sbjct: 26  GMKDEDFK--KPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGI 83

Query: 95  RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149
                 +      R +    +  +++ +  D +V  + CDK TP  LMAA   ++P I +
Sbjct: 84  AMGHDGMLYSLPSREIIADAVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFV 143

Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209
           SGGPM  G  K +L   G  L  A  + A      E   E   +A P+ G C+ M TA S
Sbjct: 144 SGGPMEAG--KTKLASHGLDLVDAMVIAADSTASDEKVAEYERSACPTCGSCSGMFTANS 201

Query: 210 MNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVR-------QDIRPSQIMTRQ 262
           MN L EALG++LPG  S  A + +R Q+    G+ I +L +       + + P  I   +
Sbjct: 202 MNCLTEALGLALPGNGSTLATHSDREQLFLTAGRTIVELCKRYYGENDESVLPRSIANFK 261

Query: 263 AFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMP-AGKYLG 321
           AFENA+ +  A+G S+N   HL+A A+   V   L D  R+   VP L    P   KY  
Sbjct: 262 AFENAMMLDIAMGGSTNTILHLLAAAQEGEVAFDLRDIDRLSRKVPQLCKVAPNIQKYHM 321

Query: 322 EGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNSLTSNTD------------- 368
           E  HRAGG+ S++  L + G LH D  TV  +++ E ++    + TD             
Sbjct: 322 EDVHRAGGIFSILGSLARGGLLHTDLPTVHSRSMEEAIAKWDITQTDDEAVHTFFKAGPA 381

Query: 369 ------------------------VIHPFDTPLKHRAGFIVLSGNF-FDSAIMKMSVVGE 403
                                    I  F+       G  VL GN   D  ++K + V E
Sbjct: 382 GIPTQTAFSQSTRWETLDDDRENGCIRSFEHAYSQEGGLAVLYGNIALDGCVVKTAGVDE 441

Query: 404 AFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSA 463
           +            + FE  A +FE  +     I   A ++    I++IR  G  G PG  
Sbjct: 442 SI-----------HVFEGTAKIFESQDSAVRGI--LADEVKAGDIVIIRYEGPKGGPGMQ 488

Query: 464 EVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLK 522
           E+  + P + L  +G+  +   L DGR SG ++  SI + SPEAA GG + L++  D++ 
Sbjct: 489 EM--LYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGDKVL 546

Query: 523 VDLNTRTVNLLIDDAEMAQRRRE 545
           +D+  R++NLL+ D E+AQRR E
Sbjct: 547 IDIPNRSINLLVSDEELAQRRVE 569


Lambda     K      H
   0.319    0.135    0.407 

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: 860
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 594
Length of database: 613
Length adjustment: 37
Effective length of query: 557
Effective length of database: 576
Effective search space:   320832
Effective search space used:   320832
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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