GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Rhodobacter viridis JA737

Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate WP_110805878.1 C8J30_RS10880 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_003217355.1:WP_110805878.1
          Length = 352

 Score =  221 bits (564), Expect = 2e-62
 Identities = 128/316 (40%), Positives = 180/316 (56%), Gaps = 22/316 (6%)

Query: 10  EAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGS 69
           +A  +L LI +  F       FL+V N   V  + +  A ++ GMT VIIT GIDLSVGS
Sbjct: 21  QARTYLALILVFGFFAFMAPNFLSVANSVIVAKHAALTAFLAIGMTFVIITGGIDLSVGS 80

Query: 70  ILGAASVVMGLL------MDEKGLSPFLSVVIGL---AVGVGFGLANGLLITKARLAPFI 120
            +G  ++V G L      +   G   F ++ I L    VGV  G  NG+LITK  +APFI
Sbjct: 81  TVGLCAMVSGWLILYGIDLGAMGTMQFNTLEIALLVMCVGVFVGFVNGILITKLNVAPFI 140

Query: 121 STLGMLSVGRGLAYVMSGGWPISPFPE----------SFTVHGQGMVGPVPVPVIYMAVI 170
           +TLG L + RG A + SGG     FP           SF   G G    +PV +  +  +
Sbjct: 141 ATLGTLYIARGAALLSSGG---RTFPNLSGNADYGSASFPGIGAGTFLGLPVQIWMLIAV 197

Query: 171 GVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWL 230
           G++A    K T  GR IYA+GGN   + L G+K +R+ + VY  +GF AA  G ++ + L
Sbjct: 198 GLVAAYIAKRTPLGRHIYAVGGNERGAALSGVKVNRVKLFVYMFSGFCAAIVGLIIASQL 257

Query: 231 GVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQ 290
             A P  G+ +EL+ IAA V+GGTSLSGG G I G  +GA ++ +L +G++++ VSSFWQ
Sbjct: 258 QAAHPATGETFELNAIAAAVLGGTSLSGGRGKIGGTIVGAFVISILSDGLVMMSVSSFWQ 317

Query: 291 QVVIGIVIIIAIAIDQ 306
            V+ G+VI+ A+ IDQ
Sbjct: 318 TVIKGLVIVAAVVIDQ 333


Lambda     K      H
   0.328    0.145    0.421 

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: 320
Number of extensions: 16
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: 313
Length of database: 352
Length adjustment: 28
Effective length of query: 285
Effective length of database: 324
Effective search space:    92340
Effective search space used:    92340
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: 49 (23.5 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