GapMind for catabolism of small carbon sources

 

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

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_109969430.1 DK846_RS13185 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_003173355.1:WP_109969430.1
          Length = 400

 Score =  207 bits (528), Expect = 4e-58
 Identities = 133/395 (33%), Positives = 206/395 (52%), Gaps = 31/395 (7%)

Query: 28  DRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYL 87
           ++ +   VWD  G++YLDF  G  V   GH +P +  A+  Q KK+         Y P  
Sbjct: 27  EKGDGVYVWDENGKQYLDFTSGWGVTCIGHANPIITEALCNQSKKIIQNPNSGATYSPAR 86

Query: 88  E-LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTL 146
             L ++ ++ +P    +      +G+EA + A+K+AR  T +   I+   ++HGRT  T+
Sbjct: 87  SRLIQLFHEILPKHLTR-IFFANSGAEANDAAIKLARKVTGKKNIISTEMSFHGRTISTV 145

Query: 147 ALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIE 206
           + TG+    +    LMPG+ +      P + IS    I             +D+AA+++E
Sbjct: 146 SATGQDVHRNKFNPLMPGYFF-----VPFNDISAVKEIID-----------QDVAAVIVE 189

Query: 207 PVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTF 266
           P+QGEGG    S +++  L  +C EHG++ IADE+Q+G  RTG LF     G  PD+ T 
Sbjct: 190 PIQGEGGVNIPSESYLLELSEVCREHGVLFIADEIQTGFFRTGPLFYSISKGAKPDIITM 249

Query: 267 AKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKAND 326
           AK IAGGFP +      EV++ +  G  GGTY GNP+ C  +  V++     ++    +D
Sbjct: 250 AKGIAGGFPFSAFAVTDEVVNGIQKGDHGGTYNGNPLGCAVSEAVIRYLIDSDIESHVSD 309

Query: 327 LGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARDKGL 385
           LG      L    EK+P+ I +VRG G +IA+EL +D          +AEIV R  D GL
Sbjct: 310 LGIDTIKRLNGWKEKYPKAITEVRGQGLLIALELTDD--------LKSAEIVTRCLDNGL 361

Query: 386 IL-LSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419
           IL L  G   +++RI   LTI   +++ GL+I+ +
Sbjct: 362 ILNLKHG---HIIRIFPALTITKQEMQTGLDILEK 393


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: 440
Number of extensions: 20
Number of successful extensions: 6
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: 400
Length adjustment: 31
Effective length of query: 395
Effective length of database: 369
Effective search space:   145755
Effective search space used:   145755
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