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_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein

Query= uniprot:A1S8Y2
         (425 letters)



>NCBI__GCF_000182725.1:WP_008507916.1
          Length = 403

 Score =  203 bits (517), Expect = 7e-57
 Identities = 141/402 (35%), Positives = 199/402 (49%), Gaps = 48/402 (11%)

Query: 23  IHPVFT---------ERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEK 73
           +HP++          ER E   +   +G  YIDFA GIAV + GH HP +   +  Q EK
Sbjct: 7   VHPLYDTYNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEK 66

Query: 74  FSHTCFMVLGYESYVAVCEKLNQ-LVPGDFAKKSALFTSGSEAVENAIKVARAYTKRAG- 131
             H   +   YE  +   EKL + LV   FA K     SG+EA+E AIK AR Y   +G 
Sbjct: 67  LWHLSNI---YE--IPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGH 121

Query: 132 -----VIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMA 186
                +I F   +HGRT+A +A  G+ A Y +G G       +  F        ++ A+ 
Sbjct: 122 PERFRIITFEGAFHGRTLATIAAGGQ-AKYLEGFGPKVEGFDQVPF-------GDEAALR 173

Query: 187 SIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGA 246
           +        A   + A I+LEP+QGEGG  A    F++ +R++CD  G++L+ DEVQTG 
Sbjct: 174 A--------AITPETAGILLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGV 225

Query: 247 GRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLAC 306
           GRTG FFA E  G+  DI   AK I GGFP+      AE    +  G  G TYGG+PL  
Sbjct: 226 GRTGKFFAHEWAGIRPDIMAIAKGIGGGFPIGACLATAEAAKGMTAGMHGTTYGGNPLGM 285

Query: 307 AAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQ-IAEVRGLGSMIAIELMENGK 365
           A   AV++V   +  +E   A    +K  +  L  RYP  ++E+RG G ++ ++ +    
Sbjct: 286 AVGNAVLDVVLADGFMENVQATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCV---- 341

Query: 366 PAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVP-ITAPDE 406
                 P        R   +LS G   NV+R+L P IT P+E
Sbjct: 342 -----VPNTSLIQALRDEHVLSVGAGDNVVRLLPPLITTPEE 378


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: 412
Number of extensions: 26
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 403
Length adjustment: 31
Effective length of query: 394
Effective length of database: 372
Effective search space:   146568
Effective search space used:   146568
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