GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Marinobacter adhaerens HP15

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Marino:GFF1380
          Length = 362

 Score =  219 bits (557), Expect = 1e-61
 Identities = 128/329 (38%), Positives = 187/329 (56%), Gaps = 24/329 (7%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           + ++ + K F K  A+ D NL   DG+    +GPSG GKTT LR+IAGLE   EG I   
Sbjct: 3   IEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFS 62

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGL----RLRRYPKDEIDRRVKEAAR 119
            + V D+  +DR +  VFQ+YAL+ HM V EN+AFGL    R  R  K EI +RVK+   
Sbjct: 63  GKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLE 122

Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179
           ++++EHL +R P +LSGGQ+QR+A+ RA+   P++ L+DEP   LDAK+R ++R  +  L
Sbjct: 123 MVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSL 182

Query: 180 QRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSM 239
              L  T+++VTHDQ EA+ L  ++VVM +G I+QVDTPL LY  P +RFV  F+G  ++
Sbjct: 183 HDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQVNV 242

Query: 240 --NFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTI 297
               +R GV  QG+    +  G                   +  L +RP  + L   T  
Sbjct: 243 LSGKIRDGVMRQGDAWIRLPEGCE---------------NDDAQLYLRPHEVRL---TQS 284

Query: 298 PEEENVLRGEVEVVEPLGAETEIHVAVNG 326
             ++  L   +E +  +GAE  I +  +G
Sbjct: 285 ASDDAHLPFRIEAINLIGAEVRIELKPDG 313


Lambda     K      H
   0.320    0.139    0.400 

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: 361
Number of extensions: 12
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: 376
Length of database: 362
Length adjustment: 30
Effective length of query: 346
Effective length of database: 332
Effective search space:   114872
Effective search space used:   114872
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