GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Thermus aquaticus YT-1

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_053767828.1 BVI061214_RS07270 aspartate carbamoyltransferase catalytic subunit

Query= BRENDA::Q5SJ15
         (301 letters)



>NCBI__GCF_001280255.1:WP_053767828.1
          Length = 301

 Score = 92.4 bits (228), Expect = 1e-23
 Identities = 96/310 (30%), Positives = 137/310 (44%), Gaps = 34/310 (10%)

Query: 10  KDLLDFSGYGPKELQALLDLA----EQLKRERYRGEDLKGKVLALLFEKPSLRTRTTLEV 65
           + LLDF G+   +L+++LD A    E L+R   +   L+G  +A +F +PS RTRT+ E+
Sbjct: 2   RHLLDFEGWSRADLESVLDTARVMREVLERPVKKVPALQGFTVATVFFEPSTRTRTSFEL 61

Query: 66  AMVHLGGHAVYLDQKQVGIGEREPVRDVAKNLERFVEGIAARVFRHETV---EALARHAK 122
           A   +    V    +   + + E  +D    LE    G+ A V R +         R  K
Sbjct: 62  AARRMSADVVSFAAQSSSLQKGESYKDTLLTLEAM--GVDAYVIRADAAGVPHQATRWVK 119

Query: 123 VPVVNALS-DRAHPLQALADLLTLKEVFGGLAGLEVAWVGD--GNNVLNSLLEVAPLAGL 179
             VVN     RAHP QAL D  TL E  G L G ++A VGD   + V  S  E+  L G 
Sbjct: 120 GVVVNGGDGQRAHPTQALLDAYTLLEALGSLEGKKIAIVGDILHSRVARSGAELFSLLGA 179

Query: 180 KVRVATPKGYEPDPGLLKRA--NAFFTHDPKEAALGAHALYTDVWTSMGQEAEREK---- 233
           +V  A P      P LL ++   A  T   +EA   A A+       M    ++E+    
Sbjct: 180 EVWCAGP------PSLLPQSLPGARLTPSLEEALEEADAV-------MALRLQKERMEAG 226

Query: 234 --RLRDF-QGFQVNGELLKLLRPEGVFLHCLPAHYGEETTEEAVHGPRSRVFDQAENRLH 290
              L D+   +Q+    L L +P+   LH  P +   E        PRS V  Q +N + 
Sbjct: 227 LVNLEDYIARYQITERRLGLAKPQAPLLHPGPMNRDVELEGTLADSPRSLVNRQVQNGVA 286

Query: 291 TAKAVLLTLL 300
              AVL  LL
Sbjct: 287 VRMAVLYHLL 296


Lambda     K      H
   0.319    0.137    0.396 

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: 200
Number of extensions: 8
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: 301
Length of database: 301
Length adjustment: 27
Effective length of query: 274
Effective length of database: 274
Effective search space:    75076
Effective search space used:    75076
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 (21.7 bits)
S2: 48 (23.1 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