GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Sphingobium czechense LL01

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_066599158.1 V473_RS00455 cell division ATP-binding protein FtsE

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>NCBI__GCF_001046645.1:WP_066599158.1
          Length = 236

 Score =  124 bits (311), Expect = 2e-33
 Identities = 71/219 (32%), Positives = 124/219 (56%), Gaps = 4/219 (1%)

Query: 1   MISIKNVNKWYG-DFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVI 59
           ++  +NV   YG D + L+D S  +  G    + G SG+GK++L+K +   +   +G + 
Sbjct: 4   IVQFENVGLRYGLDSETLSDVSFSLAGGGFYFLTGASGAGKTSLLKLLYLAQRPSRGVIR 63

Query: 60  VDGTSIAD-PKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKAL 118
           + G  +   P+  LP  R R+G+VFQ F L PHLS  DN+ +  ++V G  + E     +
Sbjct: 64  LFGEDVVTLPRKRLPGFRRRIGVVFQDFRLVPHLSAYDNIALP-LRVSGMEEGEIDAPVV 122

Query: 119 QLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDV 178
           ++L  VGL    +  P  LSGG+QQRVAIARA+   P +++ DEPT  +D +M   ++ +
Sbjct: 123 EMLNWVGLGDRGQARPATLSGGEQQRVAIARAVIGRPEILVADEPTGNVDADMARRLMTL 182

Query: 179 MVQLAHEGMTMMCVTHEMGFARKVAD-RVIFMDQGKIIE 216
              L   G T++  TH++    +V+  +++ +D+G++ +
Sbjct: 183 FEALNRLGTTIVVATHDLPLIAQVSGAQMMRLDKGRLAD 221


Lambda     K      H
   0.321    0.135    0.390 

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: 133
Number of extensions: 5
Number of successful extensions: 3
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: 244
Length of database: 236
Length adjustment: 23
Effective length of query: 221
Effective length of database: 213
Effective search space:    47073
Effective search space used:    47073
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 (21.9 bits)
S2: 46 (22.3 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