GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Neiella marina J221

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_087506594.1 CBE68_RS13315 ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_002165625.1:WP_087506594.1
          Length = 350

 Score =  194 bits (494), Expect = 2e-54
 Identities = 119/288 (41%), Positives = 170/288 (59%), Gaps = 19/288 (6%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           L++  +  RF    K  +VL  + ++   GE   L+GPSGCGKSTLL +IAGL +P  G 
Sbjct: 8   LELNQVRLRF----KQQQVLDCISLNQLTGEINCLLGPSGCGKSTLLKLIAGLIKPDSGT 63

Query: 65  IRIGGKNVVG----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120
           I + GK +      + P  R I MVFQ  AL+P L+VA+NI F L  +  PK ++Q+R+ 
Sbjct: 64  ISMAGKELSSKRNVIAPEQRQIGMVFQDLALFPHLTVAENICFGLYQQ--PKQQQQQRLQ 121

Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180
           ++  ++ ++   ++ PS LSGGQ+QRVA+ RALA +P+L L DEP S  D+ L+  +  E
Sbjct: 122 QLLELIGLTAKAEQYPSALSGGQQQRVALARALAPKPKLLLLDEPFSGFDSHLKSTLVPE 181

Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240
           ++++ +  GITS+ VTHDQ EA  L  R+AVM  G V Q  TP +IY  PA+ +VA FIG
Sbjct: 182 LRQILKHEGITSLIVTHDQHEAFALADRVAVMNDGQVHQYDTPQQIYRCPASAFVARFIG 241

Query: 241 SPTMNLLRGAVTGGQFGIQGAALNLAPPPSSA----NEVLLGVRPEHL 284
           S    L+ G VT         AL   P PS      +EV + +R E +
Sbjct: 242 SG--QLIAGKVTATAI---ETALGTLPLPSKQLAGNSEVSVLIRAEDI 284


Lambda     K      H
   0.318    0.135    0.388 

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: 271
Number of extensions: 12
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: 355
Length of database: 350
Length adjustment: 29
Effective length of query: 326
Effective length of database: 321
Effective search space:   104646
Effective search space used:   104646
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: 49 (23.5 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