GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Marivita geojedonensis DPG-138

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_085636118.1 MGEO_RS07590 thiamine pyrophosphate-binding protein

Query= BRENDA::P00893
         (574 letters)



>NCBI__GCF_002115805.1:WP_085636118.1
          Length = 522

 Score =  138 bits (348), Expect = 5e-37
 Identities = 148/561 (26%), Positives = 229/561 (40%), Gaps = 60/561 (10%)

Query: 3   MLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLA 62
           M  GA++V+++L   GVK +F   G  ++ ++DA     G+     RHE AAV+MA+G A
Sbjct: 1   MTRGADVVMQTLAAHGVKNIFALSGNQIMPLFDA-SLDAGVRLYHTRHEAAAVYMAEGYA 59

Query: 63  RATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGIS 122
           + +  +GV LVT+G G  NA+  + TA     P+++LSG       G  AFQE D V ++
Sbjct: 60  QLSRGLGVALVTAGAGLGNALGPLLTARASDTPVLLLSGDSPVGRDGQGAFQEMDQVALT 119

Query: 123 RPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESVSM 182
           + + K S  V + ED+   L KA  +A SGRPGPV V LP D+L               M
Sbjct: 120 QSLTKWSVRVTRAEDLSGTLHKAVHVALSGRPGPVHVSLPADVL----------LADTGM 169

Query: 183 RSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVE-ALNLPVVCSL 241
            S           +      L AA+ P++ V G A+ A     L E +E A + PV+   
Sbjct: 170 ISEAIAEASADTNVAALCDWLSAARAPLI-VLGPALNATRQPDLAERLEQATDAPVIVME 228

Query: 242 MGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVL 301
              G        +LG L              AD +  +G   D       A       ++
Sbjct: 229 SPRG----LKDPSLGAL--------TDVFAEADRVLLLGKPMDFTVQFGAAAPRAGWAIV 276

Query: 302 HIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIR-----DWWQQIEQ 356
           H D D  + ++                    E L+      P+D  R        +Q   
Sbjct: 277 HADRDELARAQL----------------NCSERLTLRLEADPVDVARGLSYGSGSEQSSA 320

Query: 357 WRARQCLKYDTHSE------KIKPQAVIETLWRLTKG--DAYVTSDVGQHQMFAALYYPF 408
           WR R        SE       I P  +   +    +G  D  V  D G+   +A      
Sbjct: 321 WRDRVHAACARRSEIVRQESPIDPSGLCAAVQSSLEGLPDPVVICDGGEFGQWAQA--GV 378

Query: 409 DKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPV 468
              RR IN G  G +G GL  A+  + A P  TV+ + GDG++  ++ E  TA++ +LP 
Sbjct: 379 SASRRIIN-GVSGAIGGGLCYAMAARAADPTATVIALMGDGTVGFHLGEFETAVREDLPF 437

Query: 469 LVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKL 528
           + +  N++      Q Q   +          S   +     A G  G  ++   EL   +
Sbjct: 438 VAIVGNDQRWNAEHQIQLREFGADRLHGCALSEARYDEAVAALGGFGALVTKLSELPGAI 497

Query: 529 SEALEQVRNNRLVFVDVTVDG 549
             A   + + R   ++V ++G
Sbjct: 498 EAA---IGSGRPACINVLMEG 515


Lambda     K      H
   0.319    0.135    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: 665
Number of extensions: 33
Number of successful extensions: 3
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: 522
Length adjustment: 36
Effective length of query: 538
Effective length of database: 486
Effective search space:   261468
Effective search space used:   261468
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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