GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Herbaspirillum seropedicae SmR1

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase

Query= curated2:Q8ZV07
         (383 letters)



>FitnessBrowser__HerbieS:HSERO_RS19685
          Length = 456

 Score =  193 bits (491), Expect = 7e-54
 Identities = 123/380 (32%), Positives = 188/380 (49%), Gaps = 42/380 (11%)

Query: 25  DDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPLNFATPARERFIEEFSKLL 84
           D  G  +ID +   GV  +G  NP++VEA++KQ E +    +   +  R     + S+++
Sbjct: 61  DPDGNTFIDLSAGVGVSSVGRCNPRVVEAIRKQSESLMH-SMEVNSSKRTELAAKISEIM 119

Query: 85  PPKFG---VVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFTNSFHGRTMGSLSITWNEKYK 141
           P       + F    G++A+E A+K AK+VT +  I+AF   +HG    S ++T    Y+
Sbjct: 120 PDGLRGDCITFFTQGGSDALEAAVKFAKRVTGRHQIIAFHGGYHGIWNASNALTTGTAYR 179

Query: 142 KAFEPL--------YPHVRFGKFNVPHE---------VDKLIG------EDTCCVVVEPI 178
           K F P         YP+     F+  H+         VD L+       +D   V+VEP+
Sbjct: 180 KGFGPFMGGVIHAPYPYAYRFPFDTSHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPV 239

Query: 179 QGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGK 238
           QGEGG  P +PEFL+ LR+   R GALLI DEVQ G GRTG +WA +  GV+PD+ T GK
Sbjct: 240 QGEGGYVPPSPEFLQILRKACDRSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGK 299

Query: 239 PVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREE--DVPGRAER 296
            + G +P+   V R D       G   +TFA N++  A A     +L++   D+  RA  
Sbjct: 300 GIGGDMPMAGLVMRSDLAAKIPDGSQPNTFAANSISAAVALTNISILQDPRLDLVNRAHT 359

Query: 297 IGAELAKALGDTGSRLAVRVKGMGLMLGLEL-----------RVKADQFIQPLLERGVMA 345
           +G E  + +    S     V+G GLM+G+EL           R K  + +  ++  GV+ 
Sbjct: 360 LGLEAQERIRSFNSPWVGEVRGRGLMIGIELVENRETREPLSREKLGKLMDYVVGHGVLM 419

Query: 346 LTAG--VNTLRFLPPYMISK 363
           +  G   N +R +P   I +
Sbjct: 420 IPCGRYTNVMRVMPSLTIPR 439


Lambda     K      H
   0.320    0.138    0.408 

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: 418
Number of extensions: 15
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: 383
Length of database: 456
Length adjustment: 32
Effective length of query: 351
Effective length of database: 424
Effective search space:   148824
Effective search space used:   148824
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 (21.8 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