GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Echinicola vietnamensis KMM 6221, DSM 17526

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__Cola:Echvi_2204
          Length = 240

 Score =  135 bits (339), Expect = 1e-36
 Identities = 82/234 (35%), Positives = 137/234 (58%), Gaps = 9/234 (3%)

Query: 23  IQISQMNKWY----GQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGK 78
           I+  ++ K Y     +   L+ + + + +GE +   GPSGSGKST++  I  L+   +G 
Sbjct: 5   IETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAGN 64

Query: 79  IIVDGIELTSDLKN-IDKVRS-EVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEE 136
            I++  +++   +N + ++R+ E+G VFQ FNL P  T LEN+ L P+      K + E+
Sbjct: 65  YILNNKDVSHMTENELAEIRNKEIGFVFQTFNLLPRATCLENVAL-PLIYAGYSKSDRED 123

Query: 137 TAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEV 196
            A   L+ V + ++    P +LSGGQ+QRVAIAR+L   P I+L DEPT  LD +   ++
Sbjct: 124 KAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTSYDI 183

Query: 197 LDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQI-VEQNNPHDFFHNPQ 249
           ++   +L ++G T++ VTHE   A   A+R++ + DG +  +QNNP+   +N Q
Sbjct: 184 MNLFDELHQKGNTIIMVTHEDDIAH-YAHRIVRLRDGLVETDQNNPNPTRNNFQ 236


Lambda     K      H
   0.320    0.134    0.391 

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: 139
Number of extensions: 10
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: 263
Length of database: 240
Length adjustment: 24
Effective length of query: 239
Effective length of database: 216
Effective search space:    51624
Effective search space used:    51624
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: 46 (22.3 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