GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Azospirillum brasilense Sp245

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate AZOBR_RS06555 AZOBR_RS06555 GntR family transcriptional regulator

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__azobra:AZOBR_RS06555
          Length = 404

 Score =  323 bits (829), Expect = 4e-93
 Identities = 179/402 (44%), Positives = 250/402 (62%), Gaps = 17/402 (4%)

Query: 15  TLDYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEK 74
           T+D+   F+ +  GM ASEIRELLKL+E  ++IS AGG+P P+ FP   I    +++ + 
Sbjct: 2   TVDWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQS 61

Query: 75  H--AAQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINP 132
           +  A  ALQY  ++GFTPLR  +  ++  R  I     +++ TSGSQQAL+ +G++ I P
Sbjct: 62  NSGAGGALQYTISEGFTPLREWICAYLGRR-GIQAGLDEVLVTSGSQQALEFVGKLLIGP 120

Query: 133 GDIIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTI 192
           G+ I+V  PTYL ALQAF  YEP+++ +P D EG ++  +E  L++      K K  Y +
Sbjct: 121 GEKILVTRPTYLGALQAFSPYEPQYLSVPGDAEGPDLAAVEAALEQ------KPKFFYLV 174

Query: 193 PTFQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGR--- 249
           P FQNP G T++  RR+ LL+L +++   IVED  Y ELRY GEP+  + A D       
Sbjct: 175 PDFQNPNGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGK 234

Query: 250 ---VIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGY 306
              V++ G+FSK + P  R+GWI      I +L + KQ+ DL T+T +Q++    V   +
Sbjct: 235 ITNVLFCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNF 294

Query: 307 LDKHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAV 366
            D HI ++   YK RRDAML AL EF P GV WTKPEGGMFVW  LPEG D   +L +A+
Sbjct: 295 -DSHIRRLRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAI 353

Query: 367 A-KGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRL 407
               VA+VPG AF A R  KNT+RL+F+    E+IREGI+RL
Sbjct: 354 KDANVAFVPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRL 395


Lambda     K      H
   0.318    0.137    0.398 

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: 494
Number of extensions: 26
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: 417
Length of database: 404
Length adjustment: 31
Effective length of query: 386
Effective length of database: 373
Effective search space:   143978
Effective search space used:   143978
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: 41 (21.7 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