GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Dethiosulfovibrio salsuginis USBA 82

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_085545417.1 B9Y55_RS11060 galactose/methyl galactoside ABC transporter permease MglC

Query= TCDB::Q9WXW7
         (317 letters)



>NCBI__GCF_900177735.1:WP_085545417.1
          Length = 329

 Score =  177 bits (450), Expect = 2e-49
 Identities = 116/318 (36%), Positives = 171/318 (53%), Gaps = 20/318 (6%)

Query: 17  VALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMVA 76
           V L  L V  A ++PRFL+   L+ +  Q +   +LA+G  F++I+GG  +DLS G MV 
Sbjct: 15  VVLAFLIVVIATIDPRFLSLAILRDILMQSSTRAILALGVAFILITGG--VDLSSGRMVG 72

Query: 77  LTGVMVAWLMTHGVPV--------WISVILILLFSIGA----GAWHGLFVTKLRVPAFII 124
              V+ A ++ +   V         ISVI  +L +I A    G  +G+ V KL VP FI 
Sbjct: 73  FAAVISASMLQNADYVRRFYPDMAQISVIFPILLAIAACMILGMLNGVIVAKLNVPPFIT 132

Query: 125 TLGTLTIARGMAAVI-----TKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADF 179
           TLG + +  G+ ++          PI G+   F   G G    IP+ + I LAVA++   
Sbjct: 133 TLGMMVVVYGINSIYFDMPPNNSQPIGGIRPDFTWFGSGYAGGIPVIILIALAVAILVWV 192

Query: 180 FLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPG 239
              KT+ G ++ A GGN  AA  SG+NV +  ++ + ++G L GV G + AAR       
Sbjct: 193 LFNKTLLGMNMYAIGGNREAAEVSGINVVKTLILLYAIAGALYGVAGFLEAARTGGATNN 252

Query: 240 VGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGI 299
            G+MYEL AIAS V+GG S TGG G+V G + G  I  ++   L  + V+ YW  ++ G+
Sbjct: 253 YGTMYELDAIASCVVGGVSTTGGVGTVPGVLAGVLIFGVINYGLTFIGVNPYWQLIIKGL 312

Query: 300 VIVVAVTLDILRRRLASK 317
           +IV AV  DI R+ +A K
Sbjct: 313 IIVAAVAFDI-RKYVAKK 329


Lambda     K      H
   0.328    0.143    0.424 

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: 321
Number of extensions: 21
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: 317
Length of database: 329
Length adjustment: 28
Effective length of query: 289
Effective length of database: 301
Effective search space:    86989
Effective search space used:    86989
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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