GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Halioglobus japonicus S1-36

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_084201012.1 C0029_RS15270 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::Q8ZPV2
         (408 letters)



>NCBI__GCF_002869505.1:WP_084201012.1
          Length = 426

 Score =  131 bits (329), Expect = 4e-35
 Identities = 100/288 (34%), Positives = 141/288 (48%), Gaps = 23/288 (7%)

Query: 27  RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNEPALRL 86
           R +G+R++D +GK YID+        +GH HPA+REA+ +Q+ +   +  G   E  ++L
Sbjct: 38  RSDGARVYDCEGKAYIDYVLSWGPMIMGHNHPAVREAVIKQSEK--GLSFGAPTELEIQL 95

Query: 87  AKKLIDATFA-ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT-LF 144
           A ++ +     + V   NSG EA  +A++LAR Y        +  IV F+  +HG +   
Sbjct: 96  ADRICEIMPGMDLVRMVNSGTEATMSAIRLARGYTG------RDTIVKFEGCYHGHSDSL 149

Query: 145 TVSAG------GQPTYSQDFAPLPPDIRHAAYND---LNSASALIDDNTCAVIVEPVQGE 195
            V AG      G P+     A L        YND   + +A A   D+   VIVEPV G 
Sbjct: 150 LVKAGSGALTMGVPSSPGVPAALADHTMTLTYNDPEGVRAAFAEHGDSIACVIVEPVAGN 209

Query: 196 GGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKALG 255
              IP    FL+ LRE CD   A+LI DEV TG  R G   A   +GV  D+ T  K +G
Sbjct: 210 MNCIPPEPGFLETLRECCDVSGAVLILDEVMTGF-RFGLQGAQGFFGVEADLTTLGKVVG 268

Query: 256 GGFPIGAM---LTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIIN 300
           GG P+GA        +  + + P     T  GNP+A A     LDII+
Sbjct: 269 GGMPVGAFGGKREIMEQIAPLGPVYQAGTLSGNPIAMAAGLATLDIIS 316


Lambda     K      H
   0.320    0.137    0.413 

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: 458
Number of extensions: 30
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: 408
Length of database: 426
Length adjustment: 31
Effective length of query: 377
Effective length of database: 395
Effective search space:   148915
Effective search space used:   148915
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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