GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Collimonas pratensis Ter91

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_061936170.1 CPter91_RS01725 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_001584185.1:WP_061936170.1
          Length = 327

 Score =  246 bits (629), Expect = 4e-70
 Identities = 138/311 (44%), Positives = 194/311 (62%), Gaps = 17/311 (5%)

Query: 17  LIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASV 76
           L+ + +   +T+  F T+ N  +V L V+ IAI+  G T VIIT GIDLSVGS+L  A V
Sbjct: 18  LVVLGLVFSLTSDAFFTLNNGMSVALQVTSIAILGIGATCVIITGGIDLSVGSVLALAGV 77

Query: 77  VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVM 136
           +  +++ + G+   + ++ GLAVG   G  NGL IT+ +L PFI+TLGM+ V RG+A  +
Sbjct: 78  IAAMVV-KAGMPVPVGMLCGLAVGAVCGGLNGLCITQLKLPPFIATLGMMLVARGVALQV 136

Query: 137 SGGWPISPFPESFTVHGQGMV--------GP--------VPVPVIYMAVIGVIAHIFLKY 180
           +G  P+S  PE F   G G +        GP        +P PVI M VI ++  I L  
Sbjct: 137 TGARPVSGLPEEFGTLGNGTLFRIVKETTGPFPDVVFPGIPYPVILMVVIAIVISIMLSR 196

Query: 181 TVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQG 240
           T  GR IYA+G N EA++L G+K  R+ +  Y I+G LA   G +L + L  AQPN G  
Sbjct: 197 TQFGRHIYAVGSNAEAARLSGVKVARVTLWTYVISGTLAGLTGCVLMSRLVTAQPNEGVM 256

Query: 241 YELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIII 300
           YELD IA+ VIGGTSL GG GTI G  +G+ ++G+LRNG+ + GVSSF QQ++IG+VI++
Sbjct: 257 YELDAIASAVIGGTSLIGGIGTISGTAIGSFVIGILRNGLNMNGVSSFVQQIIIGLVILL 316

Query: 301 AIAIDQIRRAK 311
            + IDQ+R  +
Sbjct: 317 TVWIDQMRNRR 327


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: 337
Number of extensions: 18
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: 327
Length adjustment: 28
Effective length of query: 285
Effective length of database: 299
Effective search space:    85215
Effective search space used:    85215
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