GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Azospirillum brasilense Sp245

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase

Query= curated2:Q1GP30
         (371 letters)



>FitnessBrowser__azobra:AZOBR_RS24065
          Length = 392

 Score = 95.9 bits (237), Expect = 2e-24
 Identities = 104/309 (33%), Positives = 138/309 (44%), Gaps = 20/309 (6%)

Query: 25  SAGADGRPLIKLSANENPLGTGEKARAAFAAVQSAPDALSRYPDPGSVELRAA----IAA 80
           +A   G  +I LS  +    T    R A  A   A D     P PG  ELRAA    +A 
Sbjct: 26  TAKGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDT-HYTPIPGRPELRAALARDVAR 84

Query: 81  KYGL--DPDRVICGNGSDELLHLAAGTYAGPGDEILYVRYGFAVYEIAARRVGA--VPVE 136
           + GL  +P+ VI   G+   L  A       GDE+L     +  YE   R  GA  VPV 
Sbjct: 85  RTGLPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVA 144

Query: 137 ADDRDFATDVDALLAAVTDRTRVVYLANPNNPTGTLATREEVGRLYAGLPQNVLFVI-DQ 195
            D      D  AL AAVT RTR ++LA P NPTG + + EE+  +     ++ L+V+ D+
Sbjct: 145 PDAATLRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVADE 204

Query: 196 AYAEYLTPDEDDGGLELAKTRPNVFVT-RTFSKIHGLAAERIGWGYASADVIAALHRIRL 254
            YA  LT D    G+          VT  + SK H +   R GW  A A ++A +  + L
Sbjct: 205 VYAS-LTFDRPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263

Query: 255 PFNVTRAG---QAAAVAALGDDDFVNRSRAHNARWRAWLAAELESLGN-HGVRVV-PSAT 309
                  G   QAA VA    D+ V   R    R R      LE+LG+  G+R + P A 
Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRR---DIALEALGSVPGLRCLKPEAG 320

Query: 310 NFLLVLFEG 318
            F+LV   G
Sbjct: 321 MFMLVDVRG 329


Lambda     K      H
   0.318    0.135    0.402 

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: 397
Number of extensions: 22
Number of successful extensions: 4
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: 371
Length of database: 392
Length adjustment: 30
Effective length of query: 341
Effective length of database: 362
Effective search space:   123442
Effective search space used:   123442
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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