GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Phaeobacter inhibens BS107

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF3828 PGA1_262p02320 putative acetolactate synthase isozyme 1 large subunit

Query= BRENDA::P08142
         (562 letters)



>FitnessBrowser__Phaeo:GFF3828
          Length = 551

 Score =  187 bits (474), Expect = 1e-51
 Identities = 159/549 (28%), Positives = 256/549 (46%), Gaps = 44/549 (8%)

Query: 14  TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73
           T  E +V  L  +G++ V GIPG   + +Y  L +S  +RHI  RHEQGAGF+A G AR 
Sbjct: 10  TVGEALVEELAARGVQHVFGIPGVHTVELYRGLGRS-DLRHITPRHEQGAGFMADGYARV 68

Query: 74  DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIG---TDAFQEVDTYGI 130
            G+P V    +GPG TN +T +A AR DS+P++ ++G   +  +G       +  D + +
Sbjct: 69  SGRPGVAFVITGPGLTNTLTPMAQARADSVPMLVVSGVNESGSLGHGMGHLHELPDQHAL 128

Query: 131 SIPITKHNYLVRHIEELPQVMSDAFRI---AQSGRPGPVWIDIPKDVQ-TAVFEIETQPA 186
           +  +   +  V   E+L   +  AF     A   RPGP  + IP DV  +A  + + Q +
Sbjct: 129 AKMVALKSEHVAAPEQLTPALDQAFAPIAGAALSRPGPTHVQIPLDVAGSAARDGDGQES 188

Query: 187 MAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMA 246
                     S   +      + AA+RPV+  GGG      ++R+LAE    P   T+ A
Sbjct: 189 APTGEQDRTVSPADLAALMQRLTAAERPVILAGGGARFCADQLRQLAEYLGAPVVQTVNA 248

Query: 247 LGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGAR-----FDDRAIGKTEQFCPNA 301
            G++   HPLS+      G  S   +++ AD+++ LG       +D  A G   Q     
Sbjct: 249 RGVM-FDHPLSVPASPSLG--SVRELIEAADMVLALGTELGPTDYDMYATGTMPQM---P 302

Query: 302 KIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRA--EWHQLVADLQREFPC 359
            +I +D+   +L +  +  + +Q DV  VL+  +   +   R+  +W   +A+  R    
Sbjct: 303 GLIRIDLCADQLAR-HRAELTVQGDVAAVLSAALAEWKPDVRSTTDWGIGLAEQTR---- 357

Query: 360 PIPKACDPL-----SHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSG 414
               A D +     +   ++NA+ A V   AI+  D  Q        Y  +RP  W  + 
Sbjct: 358 --TAAWDEIGESYRAQVMVLNALRAAV-PGAIVVGDSAQPIYAGNLYYDHDRPGGWFNAA 414

Query: 415 -GLGTMGFGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEA 473
            G G +G+G+PAAIGAA+A P+  V+C +GDG    ++ E+ TA +  L +  I+ NN  
Sbjct: 415 TGYGALGYGIPAAIGAAVAAPETPVICITGDGGAQFSLPEIMTAVDEALSITFIVWNNHG 474

Query: 474 LGLVHQQQSLFYEQGV-FAATYPGKINFMQIAAGFGLETCDLNNEADPQ---ASLQEIIN 529
              + +      + GV      P   +F   A  FG+    ++  ADPQ    +L     
Sbjct: 475 YQEIARSMQ---DVGVPVVGCDPTPPDFAATARSFGISHRAVS--ADPQEVAVALHSAAT 529

Query: 530 RPGPALIHV 538
             GP +I +
Sbjct: 530 ETGPRMIEI 538


Lambda     K      H
   0.320    0.135    0.400 

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: 803
Number of extensions: 42
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: 562
Length of database: 551
Length adjustment: 36
Effective length of query: 526
Effective length of database: 515
Effective search space:   270890
Effective search space used:   270890
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: 53 (25.0 bits)

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