GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Brucella inopinata BO1

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_002968535.1 BIBO1_RS18510 aspartate aminotransferase family protein

Query= uniprot:A1S8Y2
         (425 letters)



>NCBI__GCF_000182725.1:WP_002968535.1
          Length = 484

 Score =  178 bits (451), Expect = 4e-49
 Identities = 121/356 (33%), Positives = 179/356 (50%), Gaps = 28/356 (7%)

Query: 24  HPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLG 83
           H V  ERAE    +D  GR  +DF GG   L  GH HP++ AA  +  E+  H   +   
Sbjct: 61  HKVKVERAEGMYYYDQNGRRILDFFGGFGSLAFGHNHPRIIAARRKFQEELRHEIAIAFM 120

Query: 84  YESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVAR--AYTKRAGVIAFTSGYHG 141
            +   A+   L    PGD      L +SGSEA+E AIKVA   A  K+  ++   + +HG
Sbjct: 121 SQYAAALAYDLAACSPGDL-DMVFLGSSGSEAMEAAIKVAERAAGPKKPKIVYAENSFHG 179

Query: 142 RTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDA-MASIERIFKNDAEPSD 200
           +T   L++T                ++R EF    + V      + +IE  F++D E   
Sbjct: 180 KTKGVLSIT-------------DGGLYRGEFKLVDNTVRVPFGDITAIENAFRSDPE--- 223

Query: 201 IAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQMGV 260
           I  I+LE VQG GG   A   F ++LR+LCDR G++ +ADEVQ G GRTG F+A E  GV
Sbjct: 224 IGTIVLETVQGGGGIIQADAEFWQKLRQLCDRYGVIWVADEVQCGFGRTGKFYAFEHYGV 283

Query: 261 AADITTFAKSIAGG-FPLSGITGRAEV-MDAIGPGGLG-----GTYGGSPLACAAALAVI 313
             D+T  AKS+ GG   ++ +  R ++ M A G           T+GG   AC  A+  +
Sbjct: 284 IPDVTALAKSLGGGKAAMAAMIARRDIYMKAYGTPKTAMIHAMATFGGIGEACITAIEAV 343

Query: 314 EVFEEEKLLERSNAIGQTIKSAIGELASRYP-QIAEVRGLGSMIAIELMENGKPAP 368
            +  +E+L++ S  +G  +   + EL  RYP  + +VRG G M+ +E  +  +  P
Sbjct: 344 NILYDEQLIDNSAEVGDYLLERLKELQVRYPGLLKDVRGKGMMVGLEFHDFSQAMP 399


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: 475
Number of extensions: 24
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: 425
Length of database: 484
Length adjustment: 33
Effective length of query: 392
Effective length of database: 451
Effective search space:   176792
Effective search space used:   176792
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 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