GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gly1 in Phaeobacter inhibens BS107

Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate GFF2469 PGA1_c25010 low specificity L-threonine aldolase LtaE

Query= BRENDA::A0T1V9
         (348 letters)



>FitnessBrowser__Phaeo:GFF2469
          Length = 344

 Score =  289 bits (740), Expect = 6e-83
 Identities = 162/347 (46%), Positives = 214/347 (61%), Gaps = 6/347 (1%)

Query: 1   MIFSSDNWAGAHPAIAESLVTHAKGYASAYGTSELDRKVEERFSEVFER-DVAVFFVGTG 59
           M F+SDN   A+P I  +L     GYA  YG  E   KV     E+FE    AV+ V TG
Sbjct: 1   MHFASDNSGPANPEILTALSAANTGYAMGYGADEEMAKVTSCIREIFEAPQAAVYLVATG 60

Query: 60  TAANSLALSIANRAGGIAFCHREAHVNVDECGAPQFFSHGARLSAVGGARGKMDPAKLEA 119
           TAAN LALS  ++     FC R+AH+NVDEC  P+F++ GA+L+ V  A  KM PA L  
Sbjct: 61  TAANVLALSTLSQPWQTLFCTRQAHINVDECNGPEFYTGGAKLTLVSDA-DKMTPADLRQ 119

Query: 120 EIRRFPKENVHGGQPMAVTLTQATESGTVYSLGEIEAIASIARSQTLPLHMDGARFANAL 179
            +       VHG Q   V++TQ TE GTVY+L E+ A+  +++S  LP+H+DGARF NAL
Sbjct: 120 ALEGEENRGVHGPQRGPVSITQVTEFGTVYTLDELRALCDVSKSYGLPVHLDGARFTNAL 179

Query: 180 VSLGTTPAEMTWKRGIDLLSFGGTKNGCWCAEALVLFDPSRAQEMHFLRKRSAQLFSKSR 239
           VSLG TPAEMTWK G+D++SFGGTKNGC   EA++ FDP+ AQE  + RKR A LFSK R
Sbjct: 180 VSLGCTPAEMTWKAGVDVVSFGGTKNGCMGVEAVIFFDPAEAQEFEYRRKRGAHLFSKHR 239

Query: 240 FVAAQFDAYLAGDLWLDLARHANAMARRLADGITASAESRLAWAPDANEVFVVLKREAAS 299
           +++AQ  AYL  DLWL  A  ANA A RLA G+  +A +  +  P AN +F  L R    
Sbjct: 240 YLSAQMLAYLTDDLWLRNASAANAKAARLAAGL-RNAGAHFSHDPQANMIFAALPRATHQ 298

Query: 300 RLRQQGALFYDWEVPHDLEGSLAEDEGLFRLVTSFATRAEDVDRFVA 346
           RL   GA+++ W+    L+G+ AE+    R V  ++   + +D F+A
Sbjct: 299 RLFDAGAVYHLWD--GTLDGA-AEEAVTARFVCDWSVGDDQIDAFLA 342


Lambda     K      H
   0.320    0.132    0.394 

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: 342
Number of extensions: 13
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: 348
Length of database: 344
Length adjustment: 29
Effective length of query: 319
Effective length of database: 315
Effective search space:   100485
Effective search space used:   100485
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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