GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Paraburkholderia bryophila 376MFSha3.1

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate H281DRAFT_03959 H281DRAFT_03959 aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A

Query= SwissProt::Q38M35
         (462 letters)



>FitnessBrowser__Burk376:H281DRAFT_03959
          Length = 459

 Score =  241 bits (615), Expect = 4e-68
 Identities = 170/450 (37%), Positives = 240/450 (53%), Gaps = 13/450 (2%)

Query: 8   LAEHAARLRRRELTAVALIDTCAQHHARMEPR-LNAYKTWDGARARSAAAAVDTLLDQGQ 66
           LA+ AA L     T+ AL++T  +  A    +   A+   D   AR AA A D L   G 
Sbjct: 11  LAQLAADLAAGRTTSRALVETALERIADPAGQGAVAFMHVDADGARQAADAHDRLRAAGT 70

Query: 67  DLGPLMGLPVSVKDLYGVPGLPVFAGSDEAL--PEAWQAAGPLVARLQRQLGIVVGKTHT 124
            L PL G+PVSVKDL+ + G P  AGS      P A Q A   VARL+R   ++VG+T+ 
Sbjct: 71  VLSPLAGIPVSVKDLFDIEGQPTRAGSTVLADAPAATQDA-VAVARLKRAGAVIVGRTNM 129

Query: 125 VEFAFGGLGVNAHWGTPRNPWSPH---EHRVPGGSSAGAGVSLVQGSALLALGTDTAGSV 181
            EFAF GLG+N H+G P +P+      + R+ GGSS+GA  S+  G A +ALGTDT GS+
Sbjct: 130 SEFAFSGLGLNPHYGNPLSPYRRDVKGDERISGGSSSGAAASVADGMAAVALGTDTGGSL 189

Query: 182 RVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPA 241
           R+PA++ G  G K T  R P +G VPLS +LD+ G +  +V   A     L      +PA
Sbjct: 190 RIPAALCGLTGFKPTAARVPKQGGVPLSPTLDSFGPIGVSVACCALVDRMLAGLEPRVPA 249

Query: 242 PAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFR 301
             P  ++G+R+GV TN+  D ++P +AAAV+ A++ L  AGA V        +   DI  
Sbjct: 250 ARP--LEGVRLGVLTNYVTDGVEPEVAAAVDTALKHLEAAGAIVSEVRFASLDRLPDI-N 306

Query: 302 RGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAAR- 360
           R G +  E  A+         E+ DP V  R+   +  S+ +YL   A      A AAR 
Sbjct: 307 RFGFSPIEAYAWHRPLLEKHREQYDPRVLVRILKGQPASAADYLDLLAERDAMLAEAART 366

Query: 361 LFDDVDVLLTPTVPASPPRLAD-IGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDA 419
           L+   D ++ PTVP  PPR+A+ +   + +   N   +RN  + N    CAL++P  L  
Sbjct: 367 LWQRFDAVVAPTVPMLPPRVAELVSDDDLFGRTNALMLRNPGVFNFLDACALSLPCHLRG 426

Query: 420 NRMPVGLQLMGPPRAEARLIGIALGIEALI 449
           +  PVGL L G P A+  L+ I  G EA++
Sbjct: 427 D-APVGLMLAGAPHADDALLAIGRGAEAVL 455


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: 544
Number of extensions: 34
Number of successful extensions: 7
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: 459
Length adjustment: 33
Effective length of query: 429
Effective length of database: 426
Effective search space:   182754
Effective search space used:   182754
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