GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Cereibacter sphaeroides ATCC 17029

Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_011842390.1 RSPH17029_RS17535 aspartate aminotransferase family protein

Query= uniprot:A0A806JQF3
         (400 letters)



>NCBI__GCF_000015985.1:WP_011842390.1
          Length = 442

 Score =  205 bits (522), Expect = 2e-57
 Identities = 157/433 (36%), Positives = 219/433 (50%), Gaps = 59/433 (13%)

Query: 24  GTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHT-SNL 82
           G+ P+A A G+G  + D +GR Y+D  GG AV+ LGH + AV  A+  Q+  L    +  
Sbjct: 12  GSLPVA-AEGEGCYILDAEGRRYLDGSGGAAVSCLGHSNAAVRAALHDQLDRLAFAHTGF 70

Query: 83  YATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRL-------TGRTKLVAA 135
           + +EP   LA+ L A    +   RV+  + G+EA EAA KL+R         GR +++A 
Sbjct: 71  FTSEPAERLADRLAAA-APEGIERVYLVSGGSEAVEAALKLARQYFMEVGQPGRHRVIAR 129

Query: 136 HDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVG----------------YG-----DV 174
             ++HG T+G+LA  G   ++  FAPL  + +HV                 YG     ++
Sbjct: 130 RQSYHGNTLGALAAGGNEWRRAQFAPLLVETSHVSPCYEYRGRAEDESLEAYGLRVADEL 189

Query: 175 DALAAAVDDHTAAVFL-EPIMGESGVVVPPA-GYLAAARDITARRGALLVLDEVQTGMGR 232
           +A    +   T   F+ EP++G +   VP   GYL   R+I  R G LL+LDEV  GMGR
Sbjct: 190 EAEIQRLGPETVMAFVAEPVVGATAGAVPAVPGYLKRIREICDRHGVLLILDEVMCGMGR 249

Query: 233 TGAFFAHQHDGITPDVVTLAKGLGGGL-PIGACLAVGPAAELLTPG----LHGSTFGGNP 287
           TG  FA   DG+ PD++T+AKGLG G  PIGA L  G   + +  G     HG T+ G+ 
Sbjct: 250 TGHLFACAEDGVAPDMITIAKGLGAGYQPIGALLVQGRLYDAIAAGSGFFQHGHTYMGHA 309

Query: 288 VCAAAALAVLRVLASDGLVRRAEVLGKSLRHGI-EALG-HPLIDHVRGRGLLLGIALTAP 345
           + AAAA AVL  +    L++     G  L   + E LG HP +  +RGRGL  GI L A 
Sbjct: 310 MAAAAANAVLDEIEGRDLLQAVRRQGARLEGLLQERLGQHPHVGDIRGRGLFRGIELVAD 369

Query: 346 -------------HAK-DAEATA-----RDAGYLVNAAAPDVIRLAPPLIIAEAQLDGFV 386
                        HA+  AEA A        G  ++    D I LAPP II+ A+L+  V
Sbjct: 370 RETKEPFDPARKLHARIKAEAFAGGLICYPMGGTLDGVRGDHILLAPPFIISNAELEELV 429

Query: 387 AALPAILDRAVGA 399
             L   LDRA+ A
Sbjct: 430 DKLSGALDRALAA 442


Lambda     K      H
   0.320    0.136    0.399 

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: 549
Number of extensions: 31
Number of successful extensions: 7
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: 400
Length of database: 442
Length adjustment: 32
Effective length of query: 368
Effective length of database: 410
Effective search space:   150880
Effective search space used:   150880
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: 50 (23.9 bits)

This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 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