GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 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)



>lcl|FitnessBrowser__Putida:PP_3721 PP_3721 Arginine--pyruvate
           transaminase AruH
          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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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