GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dino:3608652
          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:

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