GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Phaeobacter inhibens BS107

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III

Query= BRENDA::Q98TS5
         (439 letters)



>lcl|FitnessBrowser__Phaeo:GFF919 PGA1_c09350 aminotransferase
           class-III
          Length = 450

 Score =  157 bits (396), Expect = 8e-43
 Identities = 125/414 (30%), Positives = 204/414 (49%), Gaps = 54/414 (13%)

Query: 60  VALERGKGVYVWDVEGRRYFDFLSAYSAVNQGHCHPKILDALKSQADKLTLTSRAFYNDV 119
           + LERG+G+YV+D +GR+Y + L+     + G+ + +++DA+  Q  KL  T   F    
Sbjct: 17  LCLERGEGIYVFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFT-HTFGGKT 75

Query: 120 LGEYEEYITKIFGYNKVLPM-----NTGVEGGETACKLARKWAYTVKGIPKYKAQIIFAA 174
               ++   K+     V        N+G +  +T  K+ R + +   G P+ K +II   
Sbjct: 76  HQPIQDLADKLAAMVPVEDAYIFFGNSGSDANDTHYKMLRYY-FNAIGKPE-KRKIITRE 133

Query: 175 GNFWGRTMSAISSSTDPSSYEGFGPFMPGFKII----PY-------NDLPA--LERALQ- 220
             + G T++A S ++ P++   F   +    I+    P+       N+  A  +ER LQ 
Sbjct: 134 RGYHGVTVAAGSLTSLPANLAHFDAPLEALSILRADSPHYYTARQGNETEAQFVERILQN 193

Query: 221 --------DPN-VAAFMVEPIQGEAGVIVPDEGYLTGVRQLCTAHNVLFIADEVQTGLAR 271
                   DP+ +AA +VEPI G +GVIVP +GY  G++ L   + +L  ADEV  G  R
Sbjct: 194 LEDQIISEDPDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICGFGR 253

Query: 272 TGKMLAVDHENVRPDLVILGKALSGGVYPVSAVLCDD---EVML--TIKPG--EHGSTYG 324
           TG         + PDL+   K LS   +P+SA +      E M+  T + G   HG TY 
Sbjct: 254 TGADFGCTTMGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGYTYS 313

Query: 325 GNPLGCRVAMASLEVIEEEKLAENANXMGELLRAELMK--TPSDIVTAVRGKGLLNAIVI 382
           G+P  C  A+ +LE+ E + L ++A  +G  L+ +L +  T   +V  VRGKGL+ A+ +
Sbjct: 314 GHPAACAAALKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAALEL 373

Query: 383 KQSK-----------DCDAWKVCLRLRDNGLLAKPTHGDIIRLAPPLTIKEDEI 425
             +K              A ++C   +DNGL+ +   G+ + L PPL I  +E+
Sbjct: 374 VSNKTTGASFDKGRAGATAQRLC---QDNGLILRAVAGNAVALCPPLIITREEV 424


Lambda     K      H
   0.318    0.136    0.404 

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: 498
Number of extensions: 26
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: 450
Length adjustment: 32
Effective length of query: 407
Effective length of database: 418
Effective search space:   170126
Effective search space used:   170126
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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