GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glucosaminate-lyase in Azospirillum brasilense Sp245

Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate AZOBR_RS26420 AZOBR_RS26420 amino acid deaminase

Query= reanno::pseudo3_N2E3:AO353_21740
         (405 letters)



>FitnessBrowser__azobra:AZOBR_RS26420
          Length = 432

 Score =  202 bits (513), Expect = 2e-56
 Identities = 140/378 (37%), Positives = 182/378 (48%), Gaps = 23/378 (6%)

Query: 24  DVSLPALVLHREALEHNIHWMQAFVSHSGAELAPHGKTSMTPSLFRRQLEAGAWGITLAT 83
           D++LP L L  +A   N   + A+    G  LAPH KT M P +    +EAGAWG T+A 
Sbjct: 43  DMALPVLTLDEDAFAANRDLIFAYARRHGVALAPHAKTPMAPQIASALVEAGAWGATVAN 102

Query: 84  VVQTRAAYAHGVRRVLMANQLVGAPNMALIAELLAD-PSFDFYCMVDHPDNVADLGVFFA 142
           + Q       GV R+++AN++ G  +   +  LLA  P  D     D P  V  L     
Sbjct: 103 LQQAAVLLRAGVTRLILANEIGGRASGERLGALLASHPDADLRAFADSPAAVETLAAAAR 162

Query: 143 ARG----LRLNVMIEYGVVGGRCGCRSEAEVLALAEAIKAQPG-LALTGIEGYEGVIHGD 197
           A G      L V++E G   GR G R  A V A+  A+   PG L L GI  YEG +   
Sbjct: 163 AAGRPPERPLPVLVEVG--AGRAGARDRAAVDAILAAVVRHPGLLVLDGIATYEGAVATA 220

Query: 198 QAVSGIREFAASLVRLAVQLQDSGAFAISKP-IITASGSAWYDLIAESFEAQNA-GGRFL 255
                    AA + R A       A A  +P ++TA GSA++D++        A  G   
Sbjct: 221 DPAETAANIAALMRRTAEAFALVRALAPERPLLLTAGGSAFFDMVVAGLAPVAATDGNAT 280

Query: 256 SVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEG------LRPALEVWAHVQSLPEPGFAV 309
            VLR G+   HDHG+Y+ A    LD R     G       RPAL +WA V + PEP  A+
Sbjct: 281 LVLRSGAIFFHDHGVYERA-LGALDARQGFACGGATAADFRPALRLWAEVLTRPEPELAI 339

Query: 310 IALGKRDVAYDAGLPVPLLRYRAG-VLPAVGDDVSACTVTAVMDQHAFMTVAPGVQLRVG 368
              G RD ++D GLP PL  +R G  L A G       VT + DQHAF+ V  G  L VG
Sbjct: 340 CGFGMRDASFDQGLPRPLRVHRDGTALSAEG-----LRVTRLNDQHAFVAVPAGHDLAVG 394

Query: 369 DIISFGTSHPCLTFDKWR 386
           DI+  G SHPC   D+WR
Sbjct: 395 DIVELGISHPCTCIDRWR 412


Lambda     K      H
   0.322    0.136    0.413 

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: 483
Number of extensions: 21
Number of successful extensions: 7
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: 405
Length of database: 432
Length adjustment: 32
Effective length of query: 373
Effective length of database: 400
Effective search space:   149200
Effective search space used:   149200
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 (21.9 bits)
S2: 50 (23.9 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