GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Lactobacillus silagei IWT126

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_054656019.1 CES79_RS02535 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::Q8ZPV2
         (408 letters)



>NCBI__GCF_002217945.1:WP_054656019.1
          Length = 431

 Score =  112 bits (281), Expect = 2e-29
 Identities = 95/316 (30%), Positives = 138/316 (43%), Gaps = 33/316 (10%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81
           P    +G+G+ + D    +YID+        LGHA   +   L +   R      G   E
Sbjct: 36  PLFIAKGKGAYIEDIDHNKYIDYVLSWGPLILGHADDKVVADLQDATTR--GTSYGAPTE 93

Query: 82  PALRLAKKL-IDATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHG 140
               LA+K+       E +   +SG EA  +A++LAR          +  IV F   +HG
Sbjct: 94  LETELAEKIQAIVPSLEEMRMVSSGTEATMSAIRLARGVTK------RDKIVKFIGNYHG 147

Query: 141 RT--LFTVSAGGQPTYSQDFAPLPP-----DIRHAAYNDLNSASALIDDN---TCAVIVE 190
            +  L   +  G  T+  + +P  P     D    AYND+    +L  ++      VIVE
Sbjct: 148 HSDSLLVDAGSGMATFDINTSPGVPNALAYDTLTVAYNDVEGVKSLFKEHGKEIACVIVE 207

Query: 191 PVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTT 250
           P+ G  GVIP T+ FLQ LR+   +  +LLIFDEV +G  R     A   Y + PD+ T 
Sbjct: 208 PIAGNMGVIPGTQEFLQTLRDETTKSGSLLIFDEVMSGF-RAAYHGAQSLYHIKPDLTTL 266

Query: 251 AKALGGGFPIGAMLTTQDYASVMTPG---THGTTYGGNPLATAVAGKVLDII-------- 299
            K +GGG P+G     +D    +TP     H  T  GNPLA       L+ +        
Sbjct: 267 GKVVGGGLPVGVFGGRRDLMENITPAGKIYHAGTLSGNPLAMTGGLSTLNQLSEDLYTKM 326

Query: 300 --NTPEMQNGVRQRHD 313
             NT  +  G++Q  D
Sbjct: 327 TANTKRLMAGIKQAAD 342


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: 416
Number of extensions: 26
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: 408
Length of database: 431
Length adjustment: 32
Effective length of query: 376
Effective length of database: 399
Effective search space:   150024
Effective search space used:   150024
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.

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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