GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Azohydromonas australica DSM 1124

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_029001425.1 H537_RS0133840 sulfoacetaldehyde acetyltransferase

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000430725.1:WP_029001425.1
          Length = 601

 Score =  239 bits (610), Expect = 2e-67
 Identities = 176/561 (31%), Positives = 262/561 (46%), Gaps = 38/561 (6%)

Query: 33  VALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAA 92
           V  Q++T ++A + ++   GV  +FGI G A +   D +F    +R + V HEQGAGH A
Sbjct: 9   VGPQKMTPSEAFVETMVANGVTDMFGIMGSAFMDAMD-IFAPAGIRLIPVVHEQGAGHMA 67

Query: 93  SGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADI 152
            GYA V+GR GV +  +GPG +N VT +A A     PVV +T + G    G   FQEA  
Sbjct: 68  DGYARVSGRHGVVIGQNGPGISNCVTAIAAAYWAHTPVVIVTPEAGTMGQGLGGFQEAKQ 127

Query: 153 SGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRM 212
             +    TK+   V     +       F  A S   G   ++IP+D   GQ T   P   
Sbjct: 128 LPMFQEFTKYQGHVTHPARMAEFTGRCFDRAMS-EMGPTQLNIPRDYFYGQITAEIPQPQ 186

Query: 213 ELPGYKPNTKPHSRQ-VREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVT 271
            L     +  P   Q + EAA+L+A A+ PV+  GGGV+  +  E  + LAE  G PVV 
Sbjct: 187 RL-----DRGPGGEQSLNEAAELLATAKFPVIIAGGGVVMADGVEACQALAERLGAPVVN 241

Query: 272 TLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTR---FDDRVTGKLDSFAP 328
           + +   +FP SH    G  G  G+ AA+  + R+D+++ALG+R   F       +D +  
Sbjct: 242 SYLHNDSFPASHPLWCGPLGYQGSKAAMKLISRADVVVALGSRLGPFGTLPQHGMDYWPK 301

Query: 329 EAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG-----------TIE 377
           EAK+I  D D   +G  +   V I GD KA    L+  L    +               E
Sbjct: 302 EAKIIQIDADHKMLGLVKKISVGICGDAKAAAQALVQRLGERTLACDATRAQRGDDIATE 361

Query: 378 MADWWAYLNG---VRKTYPLSYGPQSDGS--------LSPEYVIEKLGEIAGPDAVFVAG 426
            A W   L+     R  + L    ++ G         L P  V+ +L +   PD +    
Sbjct: 362 KAAWERELDAWTHERDPFSLDMIEEAKGERTPFGGHYLHPRQVLRELEKAMPPDVMVSTD 421

Query: 427 VGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMT 486
           +G     A  ++R+EKPRS+  +   G  G+A P  +GAK+A P     +  GDG + M+
Sbjct: 422 IGNINSVANSYLRFEKPRSFFAAMSWGNCGYAFPTIIGAKVAAPHRPAISYAGDGAWGMS 481

Query: 487 NQELATCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEA 546
             E  TC    IPV   + +N   G  ++ Q  FY  R+   +L +     P F  +A+A
Sbjct: 482 LMETLTCVRHDIPVTAVVFHNRQWGAEKKNQVDFYNRRFVAGELDS-----PSFAGIAKA 536

Query: 547 LGCVGLRCEREEDVVDVINQA 567
           +G  G+  +R EDV   + +A
Sbjct: 537 MGAEGIVVDRLEDVGPALQRA 557


Lambda     K      H
   0.319    0.136    0.414 

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: 954
Number of extensions: 57
Number of successful extensions: 5
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: 618
Length of database: 601
Length adjustment: 37
Effective length of query: 581
Effective length of database: 564
Effective search space:   327684
Effective search space used:   327684
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 25 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