GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Azospirillum brasilense Sp245

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate AZOBR_RS07830 AZOBR_RS07830 aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>FitnessBrowser__azobra:AZOBR_RS07830
          Length = 424

 Score =  175 bits (444), Expect = 2e-48
 Identities = 121/364 (33%), Positives = 179/364 (49%), Gaps = 13/364 (3%)

Query: 31  GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTH-YADVRGKRALRQRIAERHRRRSGQA 89
           GE+I+ L +G+PD  TP  IV   I+++    TH Y++ RG   LR+  A  ++RR    
Sbjct: 31  GEDIIDLGMGNPDQPTPQHIVDKLIEAVRDPKTHRYSNSRGIPGLRKAHAAYYKRRFNVD 90

Query: 90  VDAE-QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSE 148
           VD E + +V  G++  L  + Q + +PGD ++V  P Y  +   F   GA V  +PV   
Sbjct: 91  VDPESECIVTIGSKEGLANLAQAITSPGDIILVPNPSYPIHPFGFILAGASVRHLPVGQA 150

Query: 149 NG-------FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWM 201
           NG       F +  E       P+  A+ LN P NP+   +    +  + E C  H +++
Sbjct: 151 NGTSTDIDSFMIMLERAVRHSVPKPLALVLNYPSNPTAEVVGLDFYRPIVEFCRKHGIYI 210

Query: 202 ISDEVYSELLFDGEHV-SPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLE 260
           +SD  Y+E+ FDGE   S   +P   +      S+SK+++M GWR+G+  G   L   L 
Sbjct: 211 LSDLAYAEVFFDGEPPPSILEIPEAREVAVEFTSMSKTYSMAGWRIGFATGNKKLITALA 270

Query: 261 NLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDG 320
            +   + YG+   IQ AA  AL  P   +E +R  YR+RRD++IE LA S G     P  
Sbjct: 271 RIKSYLDYGAFTPIQVAATAALNGPQECVEQVRTMYRQRRDVMIEGLA-SAGWTVPSPSA 329

Query: 321 GMFVMVDIRP--TGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREA 378
            MF    I      L +  F+  LL    V+V  G  FG    GH+RL LV     +R+A
Sbjct: 330 SMFAWAPIPEPFAHLGSLEFSKLLLQEAKVAVAPGIGFGEYGDGHVRLALVENVHRIRQA 389

Query: 379 CRRI 382
            R I
Sbjct: 390 TRNI 393


Lambda     K      H
   0.322    0.136    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: 391
Number of extensions: 19
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: 393
Length of database: 424
Length adjustment: 31
Effective length of query: 362
Effective length of database: 393
Effective search space:   142266
Effective search space used:   142266
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