GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Jannaschia aquimarina GSW-M26

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_043919090.1 jaqu_RS11405 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000877395.1:WP_043919090.1
          Length = 464

 Score =  154 bits (390), Expect = 4e-42
 Identities = 128/422 (30%), Positives = 202/422 (47%), Gaps = 39/422 (9%)

Query: 34  RVWDVEGREYLD-FAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEI 92
           RVWD  G+E+LD  +GG+  +N G+   ++  AV  QL K+++   Q L   P     E 
Sbjct: 45  RVWDQHGKEHLDAVSGGVWTVNVGYGRTEIADAVRDQLVKMNYFA-QTLGSIPGSLFAER 103

Query: 93  MNQKVPGDFAKKTLLVTTGSEAVENAVKIAR--AATKRSGT----IAFSGAYHGRTHYTL 146
           +  K+PG    +     +GSEA E A K+ R  A T+  G     +     YHG T   +
Sbjct: 104 LLDKMPG--LSRVFYTNSGSEANEQAFKMIRQIAQTRHGGKKWKILYRDRDYHGTTIGCM 161

Query: 147 ALTGK------VNPYSAGMGLMPGHVYRALYPCPLHGISEDD----AIASIHRIFKNDAA 196
           +  G+        P++ G   +P  +    +      +S +D    A  +I  +   +  
Sbjct: 162 SAGGQDERNEQYGPFAPGFVRVPHCLEYRKHDQGWGDLSGEDYGRRAADAIEEVILAEG- 220

Query: 197 PEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQ 256
           P+ + AI +EP+   GG     P + +R++ + D++ ++L  DEV  G GRTGT F  + 
Sbjct: 221 PDTVGAICLEPITAGGGVIVPPPGYWERVQEIVDKYDLILHIDEVVCGIGRTGTWFGYQH 280

Query: 257 MGVAPDLTTFAKSIAGGF-PLAGVTGRAEVMDAV--APGG------LGGTYAGNPIACVA 307
            GV PD+ T AK +A G+  ++ V    EV D    AP           T+ G     VA
Sbjct: 281 YGVRPDIVTMAKGVASGYAAISCVATTEEVFDTFKSAPDDPMNFFRAVSTFGGCAAGPVA 340

Query: 308 ALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNK 367
           AL+ +++ E E+LL+    +G++L D L A+AE+H  IGDVRG G    IEL  D D  +
Sbjct: 341 ALKNMEIIETEDLLRNTQAMGERLLDNLHALAERHAAIGDVRGKGLFCGIELVADRDTRE 400

Query: 368 --PDAKLTAEIVARARDKGLILLSCG---PYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
             P+A++ A I A    +G ++ +     P  N   +  P  I  A     ++ I+   D
Sbjct: 401 PLPEAQVKA-IAADCMQQGYVIGASNRSVPKRNNCLLFSPALIATA---DDIDAITASVD 456

Query: 423 EA 424
           EA
Sbjct: 457 EA 458


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: 464
Number of extensions: 29
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: 426
Length of database: 464
Length adjustment: 32
Effective length of query: 394
Effective length of database: 432
Effective search space:   170208
Effective search space used:   170208
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.

Links

Downloads

Related tools

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