GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Collimonas pratensis Ter91

Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_061945961.1 CPter91_RS07485 ribose ABC transporter permease

Query= TCDB::Q9X050
         (331 letters)



>NCBI__GCF_001584185.1:WP_061945961.1
          Length = 328

 Score =  231 bits (590), Expect = 1e-65
 Identities = 131/302 (43%), Positives = 183/302 (60%), Gaps = 12/302 (3%)

Query: 24  ILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSVGSILGFSG 83
           +LL L++ F+ +S  F T++N  II +Q +VN+ +A GMTFVILT GIDLSVG+IL  + 
Sbjct: 30  VLLLLVLGFALMSENFFTVQNLSIITQQASVNIVLAAGMTFVILTAGIDLSVGAILA-AA 88

Query: 84  AVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRFNIPPFVATLGT 143
           AV A L          G+            G+  G  +GL NG +I    +PPF+ TLG 
Sbjct: 89  AVVAMLASLSPQFGMLGIAA----------GIGFGLLLGLANGALIAFMRLPPFIVTLGA 138

Query: 144 MTAVRGFIMLLTKGHPITRLGDSFDFIGSGWFLGIPMPVWIAAIATGVGIFILRKTQFGR 203
           +TA+RG   LL     +      F FIG+   LG+P  V IA +   +  FILR+T  G 
Sbjct: 139 LTAMRGLARLLADDKTVFNPDLPFAFIGNDSLLGVPWLVIIALVVVALSWFILRRTVIGV 198

Query: 204 YVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQP-NAGLMYELD 262
            +YAVGGN +AA LSG+      L+VYA+SG+L+ +  ++  +RL +A     G  YELD
Sbjct: 199 QIYAVGGNHEAARLSGIKVWKVLLFVYAVSGLLAGLGAVMTASRLSAANGLQLGQSYELD 258

Query: 263 AIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFIIIAAVIA 322
           AIAA ++GG S +GG G++ GT++GALII VL +GLVL+GVS  WQ + KG +II AV  
Sbjct: 259 AIAAVILGGTSFTGGVGSIGGTLIGALIIAVLTNGLVLLGVSDIWQYIIKGIVIIGAVAL 318

Query: 323 EK 324
           ++
Sbjct: 319 DR 320


Lambda     K      H
   0.327    0.144    0.427 

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: 416
Number of extensions: 22
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: 331
Length of database: 328
Length adjustment: 28
Effective length of query: 303
Effective length of database: 300
Effective search space:    90900
Effective search space used:    90900
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