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_5299 PP_5299 glutamate-putrescine ligase

Query= BRENDA::P36205
         (439 letters)



>FitnessBrowser__Putida:PP_5299
          Length = 460

 Score =  191 bits (485), Expect = 4e-53
 Identities = 139/448 (31%), Positives = 224/448 (50%), Gaps = 35/448 (7%)

Query: 14  NVRFIRLQFTDINGTLKNLEITPDVFLESWEDGIMF---------DGSSIEGF---VRIE 61
           + +++ L  +D+NG ++   I      + +E GI           +GS++E     + I 
Sbjct: 23  DTQYVDLLISDMNGVVRGKRIERASLHKVYEKGINLPASLFALDINGSTVESTGLGLDIG 82

Query: 62  ESDMYLKPVLDTFAVLPWTVDGAKSARVICDVYTPDGKPFEGDPRYRLRRMMEKAEQLGY 121
           ++D    P+  T +  PW      +A+++  ++  DG+PF  DPR  LR+++ K + LG 
Sbjct: 83  DADRICFPIPGTLSDEPW--QKRPTAQLLMTMHELDGQPFFADPREVLRQVVSKFDDLGL 140

Query: 122 TPYAGPEMEFFILPI-NEKGEPVPEFLDHGG-------YFDLLPLSKVEEIRRDIAIALE 173
           T  A  E+EF+++   N  G P P      G        + +  L +  +  +D+  A +
Sbjct: 141 TICAAFELEFYLIDQDNLNGRPQPPRSPISGKRPQSTQVYLIDDLDEYADCLQDMLEAAK 200

Query: 174 KMGITVEATHHEVAPSQHEVDFRYDTF-LRTADNAQTVKLVIKTMAIFHGYHATFMPKPF 232
           + G+  +A   E AP+Q EV+  +    L+  D A  +K +IK +A  H    TFM KP+
Sbjct: 201 EQGLPADAIVKESAPAQFEVNLHHVADPLKACDYAILLKRLIKNVAYDHEMDTTFMAKPY 260

Query: 233 YGVNGSGMHVHMSLF--RGDKNAFYDPDDPLGLSKELRYFVGGILKHAKALAAVTNPTIN 290
            G  G+G+HVH+SL   +  KN F   DDPL  S  LR+ +GG+L+   A  A   P IN
Sbjct: 261 PGQAGNGLHVHISLLDKKTGKNIFAS-DDPLQ-SDTLRHAIGGVLETMPASMAFLCPNIN 318

Query: 291 SYKRLVPGYEAPVYISWSVGNRSALIRIPKARGKATRLEYRSPDPSCNIYLAFAAILAAG 350
           SY+R    +  P   SW + NR+  +R+P    +  RLE+R      N YL  AAILA  
Sbjct: 319 SYRRFGAQFYVPNAPSWGLDNRTVAVRVPTDSSENVRLEHRVAGADANPYLMLAAILAGV 378

Query: 351 LDGIINKIEPPAPVEENIYHMTSERREELNIESLPGSLKEAVEELKKDDVIIDALGEHIF 410
             G+ NK+EP AP+E N Y       E+L  +SLP +L++A+  L   +V+   +     
Sbjct: 379 HHGLTNKVEPEAPIEGNSY-------EQLE-QSLPNNLRDALRALDDSEVLNQYISPDYI 430

Query: 411 EKFVEAAEKDWKEFSTYVTNWELQRYLY 438
           + FV   E +  EF   +++ E   YL+
Sbjct: 431 DIFVACKESELAEFEVSISDLEYNWYLH 458


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: 468
Number of extensions: 16
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: 439
Length of database: 460
Length adjustment: 33
Effective length of query: 406
Effective length of database: 427
Effective search space:   173362
Effective search space used:   173362
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