GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Shewanella amazonensis SB2B

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 6936133 Sama_0330 N-acetylglutamate synthase (RefSeq)

Query= BRENDA::Q6V1L5
         (301 letters)



>FitnessBrowser__SB2B:6936133
          Length = 440

 Score =  130 bits (327), Expect = 6e-35
 Identities = 90/279 (32%), Positives = 150/279 (53%), Gaps = 16/279 (5%)

Query: 22  PYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGGPEINAWLGRV 81
           PY+    G+T VV  GG AM Q + + A++ D+  L  +G+R V+V+G  P+I+A L   
Sbjct: 15  PYVNAHRGKTFVVMLGGEAMVQPQFR-AIINDVALLHSLGIRIVLVYGARPQIDAALELH 73

Query: 82  GIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSR----INTTGGRAVGFCGTDGRLVL 137
           GI P +HNG+R+TD DT++V++ V  G +  DI +R    ++ T  +        G  V+
Sbjct: 74  GIAPAYHNGVRITDEDTLKVIKQV-AGALQFDITARLSMSLSNTPMQGTQLNVVSGNFVI 132

Query: 138 ARPHD-QEGIGFV--GEVNSVNSEVIEPLLERGYIPVISSVAADENGQSFNINADTVAGE 194
           A+P   ++G+ F   G V  ++   ++  L+   I ++  +AA   G+SFN+ A+ VA +
Sbjct: 133 AQPLGVEDGVDFCLSGRVRRIDVNGLKHQLDSRGIVLMGPIAASVTGESFNLTAEEVATQ 192

Query: 195 IAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGG----GMIPKVD 250
           +A  L A+K+I  +   GIL+   R   +I  L    ++++ A+   GG    G +  + 
Sbjct: 193 VAVKLKADKMIGFSSQNGILD---RNGEVIAELMPNDAQKIFAKMQEGGQACVGTLAFLK 249

Query: 251 CCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIV 289
             I +   GV   H++      ALL E+F+  GIGT IV
Sbjct: 250 ASIDACRNGVPRCHLVSYLEDGALLQELFSRDGIGTQIV 288


Lambda     K      H
   0.320    0.139    0.406 

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: 323
Number of extensions: 25
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: 440
Length adjustment: 29
Effective length of query: 272
Effective length of database: 411
Effective search space:   111792
Effective search space used:   111792
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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