GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Phyllobacterium brassicacearum STM 196

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_106714457.1 CU102_RS29025 glutamine synthetase

Query= BRENDA::O33342
         (457 letters)



>NCBI__GCF_003010955.1:WP_106714457.1
          Length = 456

 Score =  401 bits (1030), Expect = e-116
 Identities = 220/448 (49%), Positives = 283/448 (63%), Gaps = 5/448 (1%)

Query: 13  ELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTV 72
           EL+R V  G++DTV+  F DMQGRL GKR    +FV+  A      C+YLLA D+D+  V
Sbjct: 9   ELKRRVNNGEIDTVLACFVDMQGRLIGKRFHATYFVES-AHDETHGCNYLLANDIDMEPV 67

Query: 73  PGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSE-VAVSPRSILRRQ 131
           PGY  ASW  GYGD ++ PDLST+R IPWL   ALV+ D++     E +A SPRSIL+RQ
Sbjct: 68  PGYKAASWKQGYGDFIIKPDLSTIRHIPWLEKCALVLCDILDHHHHEDLAHSPRSILKRQ 127

Query: 132 LDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLR 191
           L RLK RG +A  A+ELEF +FD+ Y  A A  ++G+  AS Y  DY I  +++ + ++R
Sbjct: 128 LARLKERGYLAYFASELEFYLFDETYETARAKHWKGMNTASPYIQDYVIQMTTKEDAVMR 187

Query: 192 DIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLT 251
            IR G+  AG+  E  KGE   GQ+EI  RY EAL   D H + KNG KEIA Q GK++T
Sbjct: 188 AIRNGLFDAGIPVENSKGEWGPGQEEINVRYAEALEMADRHVVMKNGCKEIATQMGKAIT 247

Query: 252 FMAKYD-EREGNSCHIHVSLRGTDG-SAVFADSNGPHGMSSMFRSFVAGQLATLREFTLC 309
           FMAKYD    G+S H+H SL   DG + +F D    H MS + R +VAGQL    +FT  
Sbjct: 248 FMAKYDYSLAGSSSHVHNSLWSADGKTPLFYDKKAEHTMSPLMRQWVAGQLKYADDFTYF 307

Query: 310 YAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHG-QNIRVECRVPGGDVNQYLAVA 368
            AP INSYKRF   +FAPT   W LDNRT   R+ G G + IR+ECR+ G D+N YLA A
Sbjct: 308 LAPYINSYKRFQAGTFAPTKSVWSLDNRTAGFRLCGEGTKGIRIECRIGGADLNPYLAFA 367

Query: 369 ALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVA 428
            LIA GL GI+  L L  P  G+AY G  ++ +P TL +A      S +++EA GEDVV 
Sbjct: 368 GLIASGLAGIDEKLDLGPPFQGDAYGGTRLKEIPKTLREATETLARSKMLKEALGEDVVE 427

Query: 429 HYLNNARVELAAFNAAVTDWERIRGFER 456
           HY++ A+ E   ++  VTDWE  RGFER
Sbjct: 428 HYVHTAKWEQFEYDRRVTDWELHRGFER 455


Lambda     K      H
   0.321    0.137    0.417 

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: 579
Number of extensions: 27
Number of successful extensions: 6
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: 457
Length of database: 456
Length adjustment: 33
Effective length of query: 424
Effective length of database: 423
Effective search space:   179352
Effective search space used:   179352
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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