GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Marinobacter adhaerens HP15

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>FitnessBrowser__Marino:GFF1380
          Length = 362

 Score =  214 bits (545), Expect = 3e-60
 Identities = 112/256 (43%), Positives = 164/256 (64%), Gaps = 10/256 (3%)

Query: 3   SVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTI 62
           S+ ++ I K +D+ + + DINL I DG+    +GPSG GK+TL+R+IAGLE    G +  
Sbjct: 2   SIEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRF 61

Query: 63  DGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTK----KPEIDAAVRNAA 118
            G  V D+    R +  VFQ YAL+ HMT+ +N+AFGL +   K    KPEI   V++  
Sbjct: 62  SGKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLL 121

Query: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178
           +++ ++HL DR P QLSGGQ+QR+A+ RA+  +P++ L DEP   LDA +R  +R     
Sbjct: 122 EMVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRS 181

Query: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238
           LHDEL  T ++VTHDQ EA+ L+D++VV+S G +EQV +P  LY  P +RFV  F+G  +
Sbjct: 182 LHDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLG--Q 239

Query: 239 MNFMEGVVQSVTHDGV 254
           +N + G ++    DGV
Sbjct: 240 VNVLSGKIR----DGV 251


Lambda     K      H
   0.320    0.135    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: 314
Number of extensions: 8
Number of successful extensions: 2
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: 369
Length of database: 362
Length adjustment: 30
Effective length of query: 339
Effective length of database: 332
Effective search space:   112548
Effective search space used:   112548
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: 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