GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Dinoroseobacter shibae DFL-12

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate 3608652 Dshi_2045 thiamine pyrophosphate protein central region (RefSeq)

Query= curated2:Q9RQ65
         (574 letters)



>lcl|FitnessBrowser__Dino:3608652 Dshi_2045 thiamine pyrophosphate
           protein central region (RefSeq)
          Length = 592

 Score =  178 bits (452), Expect = 5e-49
 Identities = 145/571 (25%), Positives = 258/571 (45%), Gaps = 38/571 (6%)

Query: 4   LSGSEMIIQSLIDQGIKYIFGYPGGAVLDIYDSLKSTKKIKHILVRHEQGATHMADGYAR 63
           ++  E  I+ L   G+ + FG  G A++ I D L     I      HE  A  MADG+ R
Sbjct: 3   MTTEEAFIKVLQRHGVDHAFGIIGSAMMPISD-LFPEAGITFWDCAHEGSAGMMADGFTR 61

Query: 64  ATGKIGVVLVTSGPGATNSITGIATAYMDSIPIVVISGQVSSSLIGYDAFQECDMIGISR 123
           A+G++ +++  +GPG TN +T + TAY +  P+++++ Q ++  IG   FQE   + +  
Sbjct: 62  ASGRMSMMIAQNGPGITNFVTAVKTAYWNHTPLLLVTPQAANKTIGQGGFQEVAQMKLFE 121

Query: 124 PIVKHSFLVKKTEDIPITFKKAFWLASSGRPGPIVIDLPKDILNSYNKKPYIWPIEVNIR 183
            +V +   V+    +     +    A +   GP  I++P+D           W   ++I 
Sbjct: 122 DMVAYQEEVRDPSRMAEVLTRVISKAKT-LSGPAQINIPRD----------FWTQVIDIE 170

Query: 184 SYNPI----TKGHSRQIKKAIDILKLSKQPVIYAGGGVI-SANCHNELKELAEKLNIPVT 238
              PI    + G    + +A  +L  +K PVI  G GV+ S       K LAE+L+ PV 
Sbjct: 171 IPEPIEFERSPGGEASVARAAALLSEAKNPVILNGAGVVLSEGGIAASKALAERLDAPVC 230

Query: 239 TSLMALGAFPGNHPQNLQMLGMHGTYEANMAMHYADVILAIGVRFDDRTT---NNVKKYC 295
                  AFPG HP     LG +G+  A   +  ADV+LA+G R +  +T     ++ + 
Sbjct: 231 VGYQHNDAFPGGHPLFAGPLGYNGSKAAMELISEADVVLALGTRLNPFSTLPGYGMEYWP 290

Query: 296 PNATIIHIDIDPTSISKTITAHIPIVGNAKNVLQQILVFI--------NSNMFVKEFYCL 347
            +A II +DI+   I  T    + IVG+A  V + IL  +              +     
Sbjct: 291 ADAKIIQVDINSDRIGLTKKISVGIVGDAAKVARGILGQLAEDAGDAGRQERRDRIAQVK 350

Query: 348 KKWWIKIQSWKNK--------NSLNFDTNSDNIKPQSVIKTIWKLTKGKAFITSDVGQHQ 399
            +W  ++ +  ++        N+       D + P+   + I       A I+SD+G + 
Sbjct: 351 SRWAQQLSAMDHEEDDPGTTWNARARAAKPDWMSPRMAWRAITAALPRDAIISSDIGNNC 410

Query: 400 MFAALYYSFQKPRRWINSGGLGTMGFGLPAALGVKLAFPNETVICVTGDGSIQMNIQELS 459
                Y  F  PR+++  G  G  G+GLPA +G K+A P+  V+   GDG+  + + EL+
Sbjct: 411 AIGNAYPDFDAPRKYLAPGLFGPCGYGLPAIVGAKIAQPDTPVVGFAGDGAFGIAVNELT 470

Query: 460 TAMQYELP-ILILNLNNKSLGMVKQWQDIIYSGRHSHSYMKSLPNFIKLAESYGHSGISI 518
              + + P I  +   N   G  K+   + +      + +    ++  +A + G  G+ +
Sbjct: 471 AIGRGDWPAITQVVFRNYQWGAEKRNSTLWFDDNFVGTELDEEVSYAGIARACGLDGVVV 530

Query: 519 NTPKELEKKLQLALE-KLQNGHLVFVDIKID 548
            T +EL   L  A++ ++  G    +++ ++
Sbjct: 531 RTMQELTDTLATAIKAQMTEGKTTLIEVLLN 561


Lambda     K      H
   0.319    0.136    0.403 

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: 715
Number of extensions: 44
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 574
Length of database: 592
Length adjustment: 36
Effective length of query: 538
Effective length of database: 556
Effective search space:   299128
Effective search space used:   299128
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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