GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Pseudomonas fluorescens FW300-N1B4

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate Pf1N1B4_3822 2-methylaconitate cis-trans isomerase

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3822
          Length = 396

 Score =  196 bits (499), Expect = 7e-55
 Identities = 140/393 (35%), Positives = 206/393 (52%), Gaps = 41/393 (10%)

Query: 3   QTRIPCLLMRGGTSKGAYFLHDDLPA----PGPLRDRVLLAVMGSPDA--RQIDGIGGAD 56
           Q +IP   MRGGTSKG +F   DLP     PG  RD +LL V+GSPD   +QIDG+GGA 
Sbjct: 6   QIKIPATYMRGGTSKGVFFSLKDLPEVAQIPGSARDALLLRVIGSPDPYDKQIDGMGGAT 65

Query: 57  SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAAS- 115
           S TSK  I+  S + D DVDYLF QV +D+  VD+  NCGN+ A VG FA+  GLV AS 
Sbjct: 66  SSTSKTVILSKSLKADHDVDYLFGQVSIDKPFVDWSGNCGNLSAAVGSFAVSNGLVDASR 125

Query: 116 ---GASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAG-- 170
                   VR++  N G+  +A VP  +G+V+  GD  +DGV   AA + + F D A   
Sbjct: 126 IPHNGVAVVRVWQANIGKTIIAHVPITNGEVQETGDFELDGVTFPAAEVQLEFIDPAAEE 185

Query: 171 -ASCGALLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSA 224
               G++ PTGN  D +E      ++ T I+ G+P + + AED+G TG E    +  D  
Sbjct: 186 EGEGGSMFPTGNLVDDLEVPGVGTLKATLINAGIPTIFINAEDIGYTGTELQGAINGDLK 245

Query: 225 LKTRLEAIR----LQLGPRMNLGDVSQR-NVPKMCLLSAP-----RNGGTVN-------T 267
                E IR    L++G   +L + ++R + PK+  ++ P      +G  +         
Sbjct: 246 ALAMFETIRAYGALRMGLIQHLDEAAKRQHTPKVAFVAKPADYIASSGKKIAATDIDLLV 305

Query: 268 RSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTV--EI 325
           R+    + H ++    AV++ TA  I G++     +  G +R  +   HPSG   V  E 
Sbjct: 306 RALSMGKLHHAMMGTAAVAIGTAAAISGTLVN--LAAGGIERNAVRFGHPSGTLRVGAEA 363

Query: 326 SLEHG--VIKGCGLVRTARLLFDGVVCIGRDTW 356
           S  +G   +K   + R+AR+L +G V +  D++
Sbjct: 364 SQVNGEWTVKKAIMSRSARVLMEGFVRVPGDSF 396


Lambda     K      H
   0.320    0.138    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: 373
Number of extensions: 30
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: 361
Length of database: 396
Length adjustment: 30
Effective length of query: 331
Effective length of database: 366
Effective search space:   121146
Effective search space used:   121146
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: 50 (23.9 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