GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Herbaspirillum seropedicae SmR1

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate HSERO_RS12800 HSERO_RS12800 aspartate aminotransferase

Query= BRENDA::Q9ZEX3
         (397 letters)



>FitnessBrowser__HerbieS:HSERO_RS12800
          Length = 431

 Score =  137 bits (346), Expect = 5e-37
 Identities = 110/365 (30%), Positives = 166/365 (45%), Gaps = 27/365 (7%)

Query: 3   PRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIA--ANLAGLS 60
           PR++ L PY F     L   A +   D+  I++S+G P  A P  + + +   A      
Sbjct: 42  PRIERLPPYVFNITAELKMAARRRGEDI--IDMSMGNPDGATPPHIVEKLVEVAQRPDTH 99

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGALV 120
            Y S+KG P LR+AI+ W   RY +   DP+SE +  +GS+E L       +D   G  V
Sbjct: 100 GYSSSKGIPRLRRAIAHWYRSRYEVDF-DPDSEAIVTIGSKEGLAHLMLATLDK--GDTV 156

Query: 121 VCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAG 180
           + PNP Y I+   A++AGA    V   P  DF     R   E + + +++ +  P NP  
Sbjct: 157 LVPNPSYPIHIYGAVIAGANIRSVRMSPGVDFFDELERAVRESYPKPKMMILGFPSNPTA 216

Query: 181 NVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDE-DTPPLGSLQAARRLGRDRYTNLVA 239
             + LE +  + +L+  H  ++     Y++I  D    P +  +  AR +        V 
Sbjct: 217 QCVELEFFERVVKLAREHQILVVHDLAYADITFDGWKAPSIMQVPGAREVA-------VE 269

Query: 240 FSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRKT 299
           F +LSK  N+ G R GF+ G+A L+A     ++YH       V  A+IAA    + C   
Sbjct: 270 FFTLSKSYNMAGWRIGFMVGNARLVAALARIKSYHDYGSFTPVQVAAIAALEGDQSC--V 327

Query: 300 AQYRAKFEAVLPILQNVLD-----VRAPQASFYLWAGTPG-----SDTAFARELYGRTGV 349
            + RA +E    +L   L      V  P+AS Y+WA  P          FAR L  +  V
Sbjct: 328 EEIRANYERRRNVLVKGLHEAGWMVDVPKASMYIWARIPEPYRQFGSLEFARILLEQAKV 387

Query: 350 TVLPG 354
            V PG
Sbjct: 388 CVSPG 392


Lambda     K      H
   0.321    0.135    0.412 

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: 468
Number of extensions: 23
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: 397
Length of database: 431
Length adjustment: 31
Effective length of query: 366
Effective length of database: 400
Effective search space:   146400
Effective search space used:   146400
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 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