GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Dyella japonica UNC79MFTsu3.2

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3307
          Length = 426

 Score =  155 bits (393), Expect = 2e-42
 Identities = 115/334 (34%), Positives = 156/334 (46%), Gaps = 25/334 (7%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNE 81
           PF   R +G+ LWD +GK YID+ G      +GH HP +REA+          G     E
Sbjct: 32  PFFTARADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVKDGLSFGTPCPAE 91

Query: 82  PVL-RLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHG 140
             +     +L+ +   D V   NSG EA  +A++LAR        + +S IV F+  +HG
Sbjct: 92  ITMAETITRLVPSV--DMVRMVNSGTEATMSAIRLARG------ATGRSKIVKFEGCYHG 143

Query: 141 R-TLFTVSAG------GQPAYSQDFAPLPADIRHA-AYNDINSASALIDD---STCAVIV 189
               F V AG      G P  S       AD+    AYND+ +A AL  +       +I+
Sbjct: 144 HGDSFLVKAGSGALTFGVPT-SPGVPKAAADLTLTLAYNDLAAAEALFAEHGADIAGLII 202

Query: 190 EPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLT 249
           EP+ G    +P  + +LQGLR LC RH ALLIFDEV TG  R     A  HYG+TPDL T
Sbjct: 203 EPVAGNMNCIPPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGITPDLST 261

Query: 250 TAKALGGGFPVGALLATEE-CARVMTVGT--HGTTYGGNPLASAVAGKVLELINTPEMLN 306
             K +GGG PVGA     E   ++   G      T  GNP+A A    +LELI      +
Sbjct: 262 FGKIIGGGMPVGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAMLELIQEAGFYD 321

Query: 307 GVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIG 340
            +  R     + L  +    G+      +G + G
Sbjct: 322 RLAARTRLLADGLQAVADGEGVPFSTNRVGAMFG 355


Lambda     K      H
   0.319    0.135    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: 442
Number of extensions: 20
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 406
Length of database: 426
Length adjustment: 31
Effective length of query: 375
Effective length of database: 395
Effective search space:   148125
Effective search space used:   148125
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 17 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