GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Methanospirillum lacunae Ki8-1

Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_109969430.1 DK846_RS13185 aspartate aminotransferase family protein

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_003173355.1:WP_109969430.1
          Length = 400

 Score =  214 bits (546), Expect = 3e-60
 Identities = 131/400 (32%), Positives = 209/400 (52%), Gaps = 38/400 (9%)

Query: 35  KGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELI-HPGFNVMMYPTYI 93
           KG+G  ++D +G++++DF    G   +GH++P + EA+  Q++++I +P       P   
Sbjct: 28  KGDGVYVWDENGKQYLDFTSGWGVTCIGHANPIITEALCNQSKKIIQNPNSGATYSPARS 87

Query: 94  ELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSFTRGFHGRTNMTMS 153
            L +    I P  H  +  F NSGAEA + A+K+ARK T ++ ++S    FHGRT  T+S
Sbjct: 88  RLIQLFHEILP-KHLTRIFFANSGAEANDAAIKLARKVTGKKNIISTEMSFHGRTISTVS 146

Query: 154 MTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFF-IASVAPET 212
            T +   ++  F P  P  +  PF                       ND   +  +  + 
Sbjct: 147 ATGQ-DVHRNKFNPLMPGYFFVPF-----------------------NDISAVKEIIDQD 182

Query: 213 VACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTYFAIEHFDV 272
           VA V++EP+QGEGG  IPS+ ++  ++  C+EHG++F+ADEIQTGF RTG  F       
Sbjct: 183 VAAVIVEPIQGEGGVNIPSESYLLELSEVCREHGVLFIADEIQTGFFRTGPLFYSISKGA 242

Query: 273 VPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAGSPLGCAAALAVLDIIEEEG 332
            PD+IT++K +A G P S      E+++    G+ GGTY G+PLGCA + AV+  + +  
Sbjct: 243 KPDIITMAKGIAGGFPFSAFAVTDEVVNGIQKGDHGGTYNGNPLGCAVSEAVIRYLIDSD 302

Query: 333 LNERSEEIGKIIEDKAYEWKQEFP-FIGDIRRLGAMAAIEIVKDPDTREPDKTKAAAIAA 391
           +     ++G     +   WK+++P  I ++R  G + A+E+         D  K+A I  
Sbjct: 303 IESHVSDLGIDTIKRLNGWKEKYPKAITEVRGQGLLIALELT--------DDLKSAEIVT 354

Query: 392 YANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILE 431
               NGL+L     +G+IIR    L I+   +  GL ILE
Sbjct: 355 RCLDNGLILNLK--HGHIIRIFPALTITKQEMQTGLDILE 392


Lambda     K      H
   0.319    0.136    0.393 

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: 393
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: 436
Length of database: 400
Length adjustment: 32
Effective length of query: 404
Effective length of database: 368
Effective search space:   148672
Effective search space used:   148672
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: 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