GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Shewanella loihica PV-4

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__PV4:5210167
          Length = 265

 Score =  194 bits (493), Expect = 2e-54
 Identities = 105/252 (41%), Positives = 155/252 (61%), Gaps = 2/252 (0%)

Query: 7   EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66
           + +L V  IS  FGG++AL+DV   ++RG V+ +IGPNGAGKT+  N I+G Y P  GT 
Sbjct: 3   DTILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGTI 62

Query: 67  ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGR-HIRTGSGLFGAVFRTK 125
               +       +  A  GI RTFQN+ LF  M+ L+N+MVGR H+   + L G ++   
Sbjct: 63  HFDNQDVTHLRPNARADLGIGRTFQNLALFGHMSVLDNIMVGRHHLMKNNWLTGPLYWAS 122

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
             + EE A  ++ +E++D++ I       A TLSYG ++R+E+ARA+A +P+LI LDEP 
Sbjct: 123 PAQKEELAHRRQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELARAMALNPKLILLDEPM 182

Query: 186 AGMNATEKVQL-RELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244
           AGMN  EK  + R ++D       T+++IEHD+ +VM +   V VLD+GK++  G P  V
Sbjct: 183 AGMNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMVLDFGKKLISGLPEAV 242

Query: 245 QKNEKVIEAYLG 256
             +E V +AYLG
Sbjct: 243 MADEHVRQAYLG 254


Lambda     K      H
   0.319    0.137    0.384 

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: 193
Number of extensions: 8
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: 260
Length of database: 265
Length adjustment: 25
Effective length of query: 235
Effective length of database: 240
Effective search space:    56400
Effective search space used:    56400
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 (21.7 bits)
S2: 47 (22.7 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