GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Pseudomonas fluorescens FW300-N1B4

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Pf1N1B4_1101 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= SwissProt::Q38M35
         (462 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101
          Length = 483

 Score =  175 bits (443), Expect = 3e-48
 Identities = 142/470 (30%), Positives = 218/470 (46%), Gaps = 40/470 (8%)

Query: 6   LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65
           L+LAE A  L  ++ ++  L        A+++P+LN++ +     A   A A D     G
Sbjct: 4   LTLAEIARGLADKKFSSEELTKVLLARIAQLDPQLNSFISLTEDLALQQAKAADARRANG 63

Query: 66  QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTV 125
           +  G L+G P++ KDL+   G+    GS             +VA+L     + +GKT+  
Sbjct: 64  ES-GALLGAPIAHKDLFCTQGIRTSCGSKMLDNFKAPYDATVVAKLAAAGAVTLGKTNMD 122

Query: 126 EFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPA 185
           EFA G    ++++G  +NPW+  EH VPGGSS G+  ++       A GTDT GS+R PA
Sbjct: 123 EFAMGSANESSYYGAVKNPWNL-EH-VPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPA 180

Query: 186 SMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAAL----DTESQGLPA 241
           ++T   GLK T GR    G++  +SSLD  G L RT ED A     +      +S  +  
Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCAILLQGMAGFDPQDSTSIDE 240

Query: 242 PAP-------VRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCE 294
           P P         +QGLR+GVP  +F   +DP IA  V A+V+ L + GA V    LP+ +
Sbjct: 241 PVPDYSAGLNGSLQGLRIGVPKEYFSAGLDPRIADLVMASVEELKKLGAVVKEISLPNMQ 300

Query: 295 EAFDIFR--RGGLAASELAAYLDQHFPHKV---------------ERLDPVVRDRVRWAE 337
            A   +       A+S L+ +    F ++                E   P V+ R+    
Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEDPKNLEDLYKRSRGEGFGPEVQRRIMVGA 360

Query: 338 QVSS-----VEYLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPA 392
              S       YL+ + + +         F++VD++L PT P    +L   G   +   A
Sbjct: 361 YALSAGYYDAYYLKAQKIRRLIKNDFMAAFNEVDIILGPTTPNPAWKL---GAKNSDPVA 417

Query: 393 NMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442
                  T  +NL G   L+MP G   + +PVG+QL+ P   E RL+ +A
Sbjct: 418 AYLEDVYTITANLAGLPGLSMPAGF-VDGLPVGVQLLAPYFQEGRLLNVA 466


Lambda     K      H
   0.320    0.135    0.411 

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: 472
Number of extensions: 25
Number of successful extensions: 8
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: 462
Length of database: 483
Length adjustment: 33
Effective length of query: 429
Effective length of database: 450
Effective search space:   193050
Effective search space used:   193050
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 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 (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