GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Herbaspirillum seropedicae SmR1

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate HSERO_RS18800 HSERO_RS18800 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::psRCH2:GFF3449
         (361 letters)



>FitnessBrowser__HerbieS:HSERO_RS18800
          Length = 293

 Score =  127 bits (319), Expect = 4e-34
 Identities = 91/299 (30%), Positives = 143/299 (47%), Gaps = 30/299 (10%)

Query: 4   VNKIEQH----NPIGTDGFEFVEF--TAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLF 57
           +N IE +    NP+G DG EF+E+  T P A G      +  +MGF +  +HRS+EV L+
Sbjct: 2   MNTIENNPVPTNPLGIDGIEFIEYATTEPLALG-----AVLERMGFEQVGRHRSREVVLY 56

Query: 58  QQHDINIVLNGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFG 117
            Q ++N+++N   T       E    S  A+A RV++A +A   V   GA  + + A   
Sbjct: 57  TQGEMNVIVNADATAWAGFDHEVQATSLSAIALRVRDANEAYRRVTELGAWAIPTRAGAM 116

Query: 118 ELNIPCVEGIGGSLLYLVDRYGDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQ 177
           ELNIP V G G S++Y VDRY D SIYDVDF+         +A+  +    L   V   +
Sbjct: 117 ELNIPGVHGCGDSIIYFVDRYRDFSIYDVDFKPASQERRQTSALAGLHFFGLVQAVQPDR 176

Query: 178 MDVWSGFYERIANFREIRYFDIEGKLTGLFSRA--MTAPCGKIRIPINESADDKSQIEEF 235
           +  W  FY  +  F  +     EG+  G+  +   + +PC +  I + E       I   
Sbjct: 177 LREWIDFYSTLMGFSVLP----EGQFFGILPKGSLLVSPCRQFYIQLVEPPAGTEDI--- 229

Query: 236 IREYHGEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLR 294
              +  E +  + L T D+   VRQL+  GV F+       ++  T+++  G  T + +
Sbjct: 230 ---HWEEELLRLGLGTPDVLQAVRQLQERGVVFV-------DRAPTQISERGALTQLYK 278


Lambda     K      H
   0.320    0.139    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: 264
Number of extensions: 9
Number of successful extensions: 2
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: 293
Length adjustment: 28
Effective length of query: 333
Effective length of database: 265
Effective search space:    88245
Effective search space used:    88245
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: 48 (23.1 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