GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Echinicola vietnamensis KMM 6221, DSM 17526

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__Cola:Echvi_2204
          Length = 240

 Score =  142 bits (358), Expect = 6e-39
 Identities = 91/234 (38%), Positives = 136/234 (58%), Gaps = 11/234 (4%)

Query: 1   MIELKNVNKYY--GTHHV--LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           +IE K + K Y  G   V  LK++ + + +GE +  +GPSGSGKST +  +  L+  ++G
Sbjct: 4   IIETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAG 63

Query: 57  EVVVNNLVLNHKNK---IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
             ++NN  ++H  +    EI  K    VFQ FNL P  T L+N+ L P+     SK + E
Sbjct: 64  NYILNNKDVSHMTENELAEIRNKEIGFVFQTFNLLPRATCLENVAL-PLIYAGYSKSDRE 122

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
           + AF  LK VGL D+ +  P  LSGGQ+QRVAIAR+L      IL DEPT  LD +T  +
Sbjct: 123 DKAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTSYD 182

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAI-VEENIPSEFFSN 226
           ++++  E+ HQ   T+++VTHE   A   A RI+ + DG +  ++N P+   +N
Sbjct: 183 IMNLFDEL-HQKGNTIIMVTHEDDIA-HYAHRIVRLRDGLVETDQNNPNPTRNN 234


Lambda     K      H
   0.317    0.133    0.372 

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: 117
Number of extensions: 7
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: 242
Length of database: 240
Length adjustment: 23
Effective length of query: 219
Effective length of database: 217
Effective search space:    47523
Effective search space used:    47523
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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