GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Dechlorosoma suillum PS

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__PS:Dsui_2943
          Length = 356

 Score =  210 bits (535), Expect = 4e-59
 Identities = 110/240 (45%), Positives = 157/240 (65%), Gaps = 8/240 (3%)

Query: 1   MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60
           MA L+L D+ + +GA  V+ G+   I+ G     +GPSGCGK+TLLR IAG E+I +G++
Sbjct: 1   MAHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSI 60

Query: 61  AFDGQIVN----QLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEA 116
           A DG++V+    +L P +R I MVFQ YAL+PH+TV +N+AFG++  G ++QQ   RV A
Sbjct: 61  ALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKGGERQQ---RVAA 117

Query: 117 AAEMLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEI 176
             +++ L    E+ P +LSGGQ+QRVA+ RA+   P++ L DEP SNLD  LR    LE+
Sbjct: 118 MLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEV 177

Query: 177 AKLHRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIG 236
            ++ +    TT I VTHDQ EA  +AD I V+ +G ++Q  TP  LY  P + FVA F+G
Sbjct: 178 REILKKA-GTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVG 236


Lambda     K      H
   0.321    0.138    0.396 

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: 336
Number of extensions: 24
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: 342
Length of database: 356
Length adjustment: 29
Effective length of query: 313
Effective length of database: 327
Effective search space:   102351
Effective search space used:   102351
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: 49 (23.5 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