GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas putida KT2440

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate PP_3721 PP_3721 Arginine--pyruvate transaminase AruH

Query= CharProtDB::CH_088628
         (385 letters)



>FitnessBrowser__Putida:PP_3721
          Length = 396

 Score =  255 bits (651), Expect = 2e-72
 Identities = 151/371 (40%), Positives = 214/371 (57%), Gaps = 9/371 (2%)

Query: 19  VNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALA 78
           ++ +AL L+ +  D++ L+ G+PDFDTP  + EAA  +L  G T YA   G   LR+A+A
Sbjct: 20  IHYRALALQAEDKDILLLSVGDPDFDTPAPIVEAAIDSLRAGHTHYADVRGKLALRQAIA 79

Query: 79  EKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGV 138
            + R+ +G +V+ ++  V  G + AL+ + Q ILDPGDEVIV  P +V+Y  +    G  
Sbjct: 80  NRHRQRSGQAVSADQVTVLAGAQCALYCVAQCILDPGDEVIVAEPMYVTYEAVFGACGAK 139

Query: 139 VVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDF 198
           VV V   PE GF   P  V   ITPRT+AL +NSP+NP+GA  P+   EALA L V HD 
Sbjct: 140 VVPVPVKPENGFRVCPRDVAERITPRTRALALNSPHNPSGASLPRATWEALAELCVAHDL 199

Query: 199 YLVSDEIYEHLLYEGEHFSPGRV--APEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAM 256
           +L+SDE+Y  LLYEGEH SPG +    E T T+N  +K+ AMTGWR+G+  G   +   +
Sbjct: 200 WLISDEVYSELLYEGEHVSPGSLPGMAERTATLNSLSKSHAMTGWRMGWVVGSTALATHL 259

Query: 257 ASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTAL-GLKAV 315
            +++           Q A + AL   E     ++  REAYR+RRDL+ E L    GLKA+
Sbjct: 260 ENLALCMLYGLPDFVQDAAVVAL---EHPLPELDAMREAYRQRRDLVCEQLAGCPGLKAL 316

Query: 316 RPSGAFYVLMDTSPIAPDEVRAAERLLEA-GVAVVPGTDF--AAFGHVRLSYATSEENLR 372
           +P G  +V++D           A+ LL++ GV+V+ G  F  +A GH+RL      E L 
Sbjct: 317 KPDGGMFVMLDIRETGVSAQAFADYLLDSQGVSVLAGEAFGPSAAGHIRLGLVLGNEALV 376

Query: 373 KALERFARVLG 383
            A +R AR  G
Sbjct: 377 DACQRIARCAG 387


Lambda     K      H
   0.317    0.133    0.379 

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: 392
Number of extensions: 10
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: 385
Length of database: 396
Length adjustment: 31
Effective length of query: 354
Effective length of database: 365
Effective search space:   129210
Effective search space used:   129210
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 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