GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Desulfoscipio geothermicus DSM 3669

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase

Query= uniprot:A1S8Y2
         (425 letters)



>NCBI__GCF_900115975.1:WP_092482996.1
          Length = 396

 Score =  230 bits (586), Expect = 7e-65
 Identities = 147/401 (36%), Positives = 212/401 (52%), Gaps = 41/401 (10%)

Query: 30  RAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGYESYVA 89
           R E A +WD +GRE++DF GGIAV + GH HP V  A+ EQ  +  H   +      Y+ 
Sbjct: 27  RGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVSNLY-----YIE 81

Query: 90  VCEKLNQLVPGDFAKKSALF-TSGSEAVENAIKVARAYTKRAG------VIAFTSGYHGR 142
              +L +L+  +       F  SG+EA E AIK+AR + K+        +I     +HGR
Sbjct: 82  PQARLAELLVQNSCCDRVFFCNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGR 141

Query: 143 TMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDAEPSDIA 202
           T+AA+  TG+   Y +G   +        F       ++ DA+   ER     A      
Sbjct: 142 TLAAITATGQ-PKYQQGFEPLPPGFKYVPF-------NDPDAL---ER-----AIGPHTC 185

Query: 203 AIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQMGVAA 262
           A++LEPVQGEGG YAA   ++  +RELCDR G++L+ DEVQ G GRTG F A +   V  
Sbjct: 186 AVMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEP 245

Query: 263 DITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIEVFEEEKLL 322
           DI T AK++ GGFP+  +  +  V  A  PG    T+GG+PLACAA LA ++    + ++
Sbjct: 246 DIITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGDGVM 305

Query: 323 ERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLTEARNRG 382
           +   A+G   K  + +LA +Y  I EVRGLG ++ +EL   G         ++   R +G
Sbjct: 306 QNCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRPG-------GDIVNRCREKG 358

Query: 383 LILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423
           L L++C    NVLR   P+    E++ R LE +    EAVL
Sbjct: 359 L-LINC-VNNNVLRFTPPLVIGTEEVDRALETV----EAVL 393


Lambda     K      H
   0.319    0.136    0.391 

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: 380
Number of extensions: 18
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: 425
Length of database: 396
Length adjustment: 31
Effective length of query: 394
Effective length of database: 365
Effective search space:   143810
Effective search space used:   143810
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 Apr 09 2024. 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