GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolB in Burkholderia phytofirmans PsJN

Align 5-deoxy-glucuronate isomerase (EC 5.3.1.-) (characterized)
to candidate BPHYT_RS28505 BPHYT_RS28505 5-deoxyglucuronate isomerase

Query= reanno::Smeli:SMc00432
         (266 letters)



>FitnessBrowser__BFirm:BPHYT_RS28505
          Length = 276

 Score =  295 bits (755), Expect = 7e-85
 Identities = 147/264 (55%), Positives = 183/264 (69%), Gaps = 3/264 (1%)

Query: 1   MSRLLVKPKAQA--GLMQEITPESAGWTYVGFALHRLQPGETAGGETGEKELCLVLVSGK 58
           MS LLVKP   A  G +  ITP SAGW YVGF +  L PG T   +TG++E+ +VLV G 
Sbjct: 1   MSDLLVKPSKHAKDGQIIHITPASAGWKYVGFDVFDLVPGATVTRDTGDREVVVVLVKGH 60

Query: 59  AKISVDGEDFGELGERMTPFEGRPYAVYVPKGSSWQAEAATALDLAVCSAPGGEGFKAKV 118
           A +  +G    E+G RM+PF+G P++VYVP  + +   A   ++L VCSAP   G   + 
Sbjct: 61  ATVGCEGLASREIGTRMSPFDGAPWSVYVPPHTRYTIVATDDVELGVCSAPAKGGLPPRF 120

Query: 119 IRPGTHPQMTRGKGTNTRYVTNIMPEDDGSAQSLLVVEVITPGGHTSSYPPHKHDEDNLP 178
           I P    Q TRG G N R+V +I+PE +  A+SLLVVE +TP G+ SSYPPH+HD D+  
Sbjct: 121 IAPDEVKQETRGAGANLRHVRHILPETE-PAESLLVVESVTPAGNWSSYPPHRHDTDDGE 179

Query: 179 AESYLEETYYHRLNPPQGFAMQRVYTDDRSLDETMAVEDGDVTLVPKGYHPVAAIHGYDS 238
            ++YLEETYYHR++PPQGFA+QRVYTDDRSLDET+A  D  V LVP+GYHPVAA HGYD 
Sbjct: 180 QQTYLEETYYHRVSPPQGFAIQRVYTDDRSLDETLAAYDKHVVLVPRGYHPVAAAHGYDL 239

Query: 239 YYLNVMAGPKRIWKFHNAREHEWL 262
           YYLNVMAGP+R W  HN   HEWL
Sbjct: 240 YYLNVMAGPRRTWHVHNEPAHEWL 263


Lambda     K      H
   0.315    0.134    0.411 

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: 314
Number of extensions: 10
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: 266
Length of database: 276
Length adjustment: 25
Effective length of query: 241
Effective length of database: 251
Effective search space:    60491
Effective search space used:    60491
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

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

Links

Downloads

Related tools

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