GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12055 in Sinorhizobium meliloti 1021

Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate SM_b20712 SM_b20712 rhizopine uptake ABC transporter substrate-binding protein precursor

Query= uniprot:A0A1N7UEK0
         (335 letters)



>FitnessBrowser__Smeli:SM_b20712
          Length = 309

 Score =  126 bits (316), Expect = 8e-34
 Identities = 87/279 (31%), Positives = 141/279 (50%), Gaps = 12/279 (4%)

Query: 16  LACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVFDGNYDALTQ 75
           +A  ++ AA  +T  V  A++     F+      ++E+    DG V+L V D   D   Q
Sbjct: 10  MAVLMSTAAHAETIGVSMALFD--DNFLTVLRSGMQEYAKTLDG-VELQVEDAQNDVAKQ 66

Query: 76  NNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADASV-----PYVG 130
            +QI+N +    DAI+  P+DT A     K A    + ++  N +  +         +V 
Sbjct: 67  QSQIQNFIAAGVDAIIVNPVDTDATAAMSKIAADAGIPLVYVNREPVNVDTLPDKQAFVA 126

Query: 131 NDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKHP--DIKIIEK 188
           +++ E G LQ + +   L GKG  V++ G +   A   R K   +V+       I+I+E+
Sbjct: 127 SNEQESGTLQTKEICKMLGGKGKAVVMMGELSNQAARMRTKDIHDVIATDECKGIEIVEE 186

Query: 189 KTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSKDVPVTSIDG 248
           +TANW R Q   L  +WL+A  +  + VI+ ND+MA+GA+QALK+ G +   V +  ID 
Sbjct: 187 QTANWSRTQGSDLMTNWLSAGLE-FDAVISNNDEMAIGAIQALKAAGRSMDSVVIGGIDA 245

Query: 249 MPDAIQA-AKKDEVTTFLQDAQAQSQGALDVALRALAGK 286
             DA+ A A  D   T  Q+A  Q +G++D AL+   G+
Sbjct: 246 TQDALAAMAAGDLDVTVFQNAAGQGKGSVDAALKLAKGE 284


Lambda     K      H
   0.314    0.130    0.373 

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: 257
Number of extensions: 17
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: 335
Length of database: 309
Length adjustment: 28
Effective length of query: 307
Effective length of database: 281
Effective search space:    86267
Effective search space used:    86267
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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