GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas litoralis 2SM5

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_900105005.1:WP_090271605.1
          Length = 417

 Score =  284 bits (726), Expect = 4e-81
 Identities = 155/407 (38%), Positives = 235/407 (57%), Gaps = 22/407 (5%)

Query: 21  QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80
           Q   + A+R E C +   +G+ YLDF  GI V +TGH HP VVAA   Q+ KL H  +  
Sbjct: 10  QSSKVCAERGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTT 69

Query: 81  LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140
           + ++P L+L E +  K+P D          GSEAVE A+++AR AT+R+  I F+G +HG
Sbjct: 70  VTHQPMLDLAERLVGKMP-DGIDSVAFSNAGSEAVEMALRLARHATRRANVIVFNGGFHG 128

Query: 141 RTHYTLALT-------GKVNPYSAGMGLMP-GHVYRALYPCPLHGISEDDA----IASIH 188
           RT    ++T          +P  AG+ + P  H +R       +G SE++A    +A + 
Sbjct: 129 RTMGAASMTTSGTKVRNAYHPMMAGVVVAPFPHSWR-------YGWSEEEATRFCLAELD 181

Query: 189 RIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRT 248
            I K   APED AA+VIEPVQGE G+Y  + AFMQ L   C +HGI+L+ DE+Q+G GR+
Sbjct: 182 HILKTQTAPEDTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRS 241

Query: 249 GTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAA 308
           G  ++ +  G+ PD+   AK +A GFPL+ +     +M     G  GGTY  N ++C AA
Sbjct: 242 GKFWSHQHFGITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAA 301

Query: 309 LEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKP 368
           L  L+V + ENL+  A   GQ+L D L  + +++P++ D+RG G M+ +E+ +  D  KP
Sbjct: 302 LATLRVMDNENLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPD--KP 359

Query: 369 DAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415
            A L A +   + ++GL+LL CG    ++R L PL + +A++   ++
Sbjct: 360 LADLAASLTTASEEEGLLLLRCGTDSQIIRWLPPLVVSEAEVDDAVQ 406


Lambda     K      H
   0.320    0.137    0.401 

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: 410
Number of extensions: 20
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: 426
Length of database: 417
Length adjustment: 32
Effective length of query: 394
Effective length of database: 385
Effective search space:   151690
Effective search space used:   151690
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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