GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Herbaspirillum seropedicae SmR1

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 HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__HerbieS:HSERO_RS05255
          Length = 347

 Score =  219 bits (559), Expect = 6e-62
 Identities = 120/306 (39%), Positives = 189/306 (61%), Gaps = 8/306 (2%)

Query: 14  FLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGA 73
           F  L+ +++F    +  F+ V+N+ +++ + +   +++   T VIITSGIDLSVG+++  
Sbjct: 40  FASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99

Query: 74  ASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLA 133
            +V+ G+++   G+   L +   +  G   G  +G++I K ++ PFI+TLGM+ + +GL+
Sbjct: 100 CAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLS 159

Query: 134 YVMSGGWPIS-PFPESFTVHGQ-GMVG------PVPVPVIYMAVIGVIAHIFLKYTVTGR 185
            V+SG  PI     E F+   Q  ++G      P+P  V+ + ++ + A I L  TV GR
Sbjct: 160 LVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGR 219

Query: 186 RIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDV 245
             +A+G N EA +L G+K D   + VYT +G +   AG ++ + L  AQP  GQGYELD 
Sbjct: 220 YTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDA 279

Query: 246 IAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAID 305
           IAA VIGGTSLSGG GTILG  +GA IM VL NG+ ++ V+  WQ VV G++II+A+ +D
Sbjct: 280 IAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLD 339

Query: 306 QIRRAK 311
            +RR +
Sbjct: 340 ILRRRR 345


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: 275
Number of extensions: 13
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: 347
Length adjustment: 28
Effective length of query: 285
Effective length of database: 319
Effective search space:    90915
Effective search space used:    90915
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 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