GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Pseudomonas putida KT2440

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate PP_5184 PP_5184 glutamylpolyamine synthetase

Query= BRENDA::P36205
         (439 letters)



>FitnessBrowser__Putida:PP_5184
          Length = 458

 Score =  197 bits (502), Expect = 4e-55
 Identities = 137/449 (30%), Positives = 223/449 (49%), Gaps = 32/449 (7%)

Query: 11  EEENVRFIRLQFTDINGTLKNLEITPDVFLESWEDGIMF---------DGSSIEGF---V 58
           E   V ++ L   D+NG ++   I      + +E GI           +GS++E     +
Sbjct: 19  EHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGL 78

Query: 59  RIEESDMYLKPVLDTFAVLPWTVDGAKSARVICDVYTPDGKPFEGDPRYRLRRMMEKAEQ 118
            I ++D    P+ DT    PW      +A+++  ++  +G+PF  DPR  LR+++ K ++
Sbjct: 79  DIGDADRICYPIPDTLCNEPW--QKRPTAQLLMTMHELEGEPFFADPREVLRQVVTKFDE 136

Query: 119 LGYTPYAGPEMEFFILPI-NEKGEPVPEFLDHGG-------YFDLLPLSKVEEIRRDIAI 170
           LG T  A  E+EF+++   N  G P P      G        + +  L +  +  +DI  
Sbjct: 137 LGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPQSTQVYLIDDLDEYADCLQDILE 196

Query: 171 ALEKMGITVEATHHEVAPSQHEVDFRYDTF-LRTADNAQTVKLVIKTMAIFHGYHATFMP 229
             ++ GI  +A   E AP+Q EV+  +    L+  D A  +K +IK +A  H    TFM 
Sbjct: 197 GAKEQGIPADAIVKESAPAQFEVNLHHVADPLKACDYAVLLKRLIKNIAYDHEMDTTFMA 256

Query: 230 KPFYGVNGSGMHVHMSLFRGDKNAFYDPDDPLGLSKELRYFVGGILKHAKALAAVTNPTI 289
           KP+ G  G+G+HVH+S+   D N  +  +DP   +  LR+ VGG+L+   A  A   P +
Sbjct: 257 KPYPGQAGNGLHVHISVLDKDGNNIFTSEDP-EQNAALRHAVGGVLETLPASMAFLCPNV 315

Query: 290 NSYKRLVPGYEAPVYISWSVGNRSALIRIPKARGKATRLEYRSPDPSCNIYLAFAAILAA 349
           NSY+R    +  P   SW + NR+  +R+P     A R+E+R      N YL  AA+LA 
Sbjct: 316 NSYRRFGAQFYVPNAPSWGLDNRTVALRVPTGSADAVRIEHRVAGADANPYLMMAAVLAG 375

Query: 350 GLDGIINKIEPPAPVEENIYHMTSERREELNIESLPGSLKEAVEELKKDDVIIDALGEHI 409
              G+ NKIEP AP+E N Y       E+L  +SLP +L++A+ EL   +++   +    
Sbjct: 376 VHHGLTNKIEPGAPIEGNSY-------EQLE-QSLPNNLRDALRELDDSEILNKYIDPKY 427

Query: 410 FEKFVEAAEKDWKEFSTYVTNWELQRYLY 438
            + FV   E + +EF   +++ E   YL+
Sbjct: 428 IDIFVACKESELEEFEHSISDLEYNWYLH 456


Lambda     K      H
   0.320    0.139    0.414 

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: 503
Number of extensions: 19
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: 439
Length of database: 458
Length adjustment: 33
Effective length of query: 406
Effective length of database: 425
Effective search space:   172550
Effective search space used:   172550
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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