GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Rhodobacter viridis JA737

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_110806203.1 C8J30_RS11905 aspartate aminotransferase family protein

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_003217355.1:WP_110806203.1
          Length = 393

 Score =  182 bits (461), Expect = 2e-50
 Identities = 140/402 (34%), Positives = 196/402 (48%), Gaps = 50/402 (12%)

Query: 30  ENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTA--YQIVPYESYVT 87
           E + L   +G+ Y+D  AGIAV   GH  P+LVA + +Q  +  H +  Y+I   E    
Sbjct: 20  EGSWLWTEDGSRYLDLGAGIAVNALGHAAPELVATLTEQAGKLWHVSNLYRIPEQER--- 76

Query: 88  LAEKINALAPVSGQAKTAFFT-TGAEAVENAVKIARAH---TGRP---GVIAFSGGFHGR 140
           LA+ + A    +  A T FFT +G EA E AVK+ R +    G+P    ++ FSG FHGR
Sbjct: 77  LADMLVA----NTFADTVFFTNSGTEACELAVKMVRKYFYEKGQPERSDILTFSGAFHGR 132

Query: 141 TYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVA 200
           +   +A  G     K GFGP      H+P+            L+A++            A
Sbjct: 133 SSAAIAAAGTEKMVK-GFGPLLPGFKHLPW----------GDLEAVKAAVTDT-----TA 176

Query: 201 AIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKP 260
           AI+ EP+QGEGG   AP+  + A+R +CD  G +++ DEVQ G ARTG+LFA +     P
Sbjct: 177 AILIEPIQGEGGIRPAPEGFLKALREICDATGTLLVFDEVQCGVARTGRLFAHEWAGVTP 236

Query: 261 DLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDK---- 316
           D+M +AK + GG PL  V+  AN       G  G TY GNPL  A    ++ I+      
Sbjct: 237 DVMMVAKGIGGGFPLGAVLATANAASGMTAGTHGSTYGGNPLGCAIGAKMIEIVTAPGFL 296

Query: 317 ESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQ 376
           E +  +A  L QRL+  L+ A   +     VRG G M+ +    P      AA AQ    
Sbjct: 297 EEVSRKAGFLRQRLEG-LVAAHPDI--FEEVRGQGLMLGLRCKLPPGDVVKAAYAQN--- 350

Query: 377 RALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDA 418
                   LLT  A  NV+R L  LTI +     A++ L+ A
Sbjct: 351 --------LLTVPAADNVLRLLPALTITEDDMAEAVRRLEAA 384


Lambda     K      H
   0.319    0.134    0.388 

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: 423
Number of extensions: 25
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: 421
Length of database: 393
Length adjustment: 31
Effective length of query: 390
Effective length of database: 362
Effective search space:   141180
Effective search space used:   141180
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