GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Pseudomonas fluorescens FW300-N1B4

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate Pf1N1B4_1107 D-galactarate dehydratase (EC 4.2.1.42)

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1107
          Length = 517

 Score =  149 bits (375), Expect = 3e-40
 Identities = 126/416 (30%), Positives = 192/416 (46%), Gaps = 42/416 (10%)

Query: 4   AAQQP----TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAE 59
           AAQ P    T EGY   DG  G RN++ +   V+C   V    V + ++ L         
Sbjct: 107 AAQAPLEGFTFEGYRNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDEL-------LP 159

Query: 60  REPPVH-LIGFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHY 108
           + P V  ++     Y  G A          + +  L  +PN+G   L +SLGCE +    
Sbjct: 160 KYPNVDDVVALTHSYGCGVAITATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQ 219

Query: 109 LVDVVRAS---GRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIG 165
           ++    +S     P          G    I+  +       ++L  +++  +  SEL++G
Sbjct: 220 VMHENDSSVDLSDPWLYRLQDSSHGFTEMIEQIMALAETRLKKLDLRRRETVPASELILG 279

Query: 166 TICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEI 225
             CGGSD  SGITANPA+G A D L+ AGAT +F E  E+    + + +RA    +  E+
Sbjct: 280 MQCGGSDAFSGITANPALGYASDLLLRAGATVMFSEVTEVRDAIYLLTSRAETEEVAQEL 339

Query: 226 VACVAKAARYYS---ILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIP 282
           V  +    RY +        +   GN  GGL+   EKSLG+  KSG+S I G++ PG+  
Sbjct: 340 VREMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERF 399

Query: 283 PTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKV 342
              GL            F     SD       +A G ++ +FTTGRG+  G A++PV+KV
Sbjct: 400 KRKGLI-----------FCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKV 448

Query: 343 CANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQ 398
                  +     +D+DAGRI  GR +++E+G E+F   + V+ G   K +T   Q
Sbjct: 449 STRTELAQRWPDLIDIDAGRIATGRASIEELGWELFHYYLDVASG---KKQTWAEQ 501


Lambda     K      H
   0.318    0.137    0.408 

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: 573
Number of extensions: 25
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: 431
Length of database: 517
Length adjustment: 33
Effective length of query: 398
Effective length of database: 484
Effective search space:   192632
Effective search space used:   192632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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