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_RS12970 AZOBR_RS12970 aspartate aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>FitnessBrowser__azobra:AZOBR_RS12970
          Length = 401

 Score =  220 bits (560), Expect = 6e-62
 Identities = 132/372 (35%), Positives = 198/372 (53%), Gaps = 15/372 (4%)

Query: 31  GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90
           G +++ L  G+PDFDTP  I  AAI ++ AG+T Y  V G  AL++ I  +  R +G   
Sbjct: 30  GRDVIGLGAGEPDFDTPDNIKDAAIKAIQAGDTKYTAVDGTPALKKAICAKFERENGLKY 89

Query: 91  DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150
             +Q+ V  G +  LY  +   L PGDEVI+  P +V+Y  +        V V   +E G
Sbjct: 90  APDQITVGVGGKQVLYNALMATLTPGDEVIIPAPYWVSYPDMVELAEGTPVFVSCPAEQG 149

Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYSE 209
           F++Q  ++   ITP+T+ + LNSP NPSGA+  R   +AL ++ + H  +W+++D++Y  
Sbjct: 150 FKLQPADLEKAITPKTKWLILNSPSNPSGAAYTRDEMKALTDVLVKHPQVWVMTDDMYEH 209

Query: 210 LLFDG-EHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCML 267
           LL+DG E V+PA + P + DRT T+N +SKS+AMTGWR+G+  GP AL   +  +     
Sbjct: 210 LLYDGIEFVTPAQVEPALYDRTLTVNGVSKSYAMTGWRIGYAGGPKALIKAMGVIQSQST 269

Query: 268 YGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFV--- 324
                  Q AA  AL  P   +      + +RRDLV+  L  + G+   +P+G  +V   
Sbjct: 270 SNPTSIAQAAAVEALNGPQDFIAERAAVFAQRRDLVVSMLNQAKGISCPKPEGAFYVYPS 329

Query: 325 ----MVDIRPTGL---SAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLRE 377
               +    P G    + + F   LL+  GV+V+ G AFG   A H R+      E L E
Sbjct: 330 CAGTIGKTTPDGKVIETDEDFVTYLLESEGVAVVQGSAFG--LAPHFRISYATSTEALEE 387

Query: 378 ACRRIALCAAEL 389
           AC+RI      L
Sbjct: 388 ACKRIQRACGNL 399


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: 400
Number of extensions: 24
Number of successful extensions: 6
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: 401
Length adjustment: 31
Effective length of query: 362
Effective length of database: 370
Effective search space:   133940
Effective search space used:   133940
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.

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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