GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Clostridium tyrobutyricum FAM22553

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_017752177.1 PN53_RS07220 D-amino acid aminotransferase

Query= curated2:Q58414
         (288 letters)



>NCBI__GCF_000816635.1:WP_017752177.1
          Length = 287

 Score =  122 bits (306), Expect = 9e-33
 Identities = 89/271 (32%), Positives = 141/271 (52%), Gaps = 9/271 (3%)

Query: 4   YLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIP 63
           Y NGK+   ++  + + D    +GDGV++   + + V+F L EHIDR ++SA  L I IP
Sbjct: 6   YYNGKYDLIENMTIPMNDRVCYFGDGVYDATYSRNHVIFALDEHIDRFFNSAGLLKIKIP 65

Query: 64  LTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLG-LDPRKCGKPTIFCIAIPMPPLLG 122
            TK+E+ +++ + ++  +  + ++   VTRG      + P    K  ++ I  P      
Sbjct: 66  YTKDELKELLNDMVKKVDSGEQFVYWQVTRGTAMRNHIFPGDDVKANVWIILKPQKVKDM 125

Query: 123 EDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEA-FLLDDKGFVVEGT 181
              +R IT+   R     L+  +K+LN L SV+A  +A+     EA F   D+  V E  
Sbjct: 126 SQKLRLITLEDTRF----LHCNIKTLNLLPSVMAAQKADEKDCQEAVFHRGDR--VTECA 179

Query: 182 GDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFIT 241
             N+ I+K+G+ KT P    IL GI R  +IK+ K+  I V E P TL +L  ADE+ +T
Sbjct: 180 HSNVSIIKDGIFKTAPADNLILPGIARAHIIKMCKKFEIPVNETPFTLEELMDADEVIVT 239

Query: 242 GTAAEIVPVFEIDGRVINNKQVGEITKKLKE 272
            +    +   EIDG  +  K   EI KKL++
Sbjct: 240 SSGQFCMTTCEIDGTPVGGK-APEIVKKLQD 269


Lambda     K      H
   0.321    0.143    0.411 

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: 226
Number of extensions: 17
Number of successful extensions: 2
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: 288
Length of database: 287
Length adjustment: 26
Effective length of query: 262
Effective length of database: 261
Effective search space:    68382
Effective search space used:    68382
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: 47 (22.7 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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