Aligments for a candidate for ilvH in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Aligments 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis