GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsB in Caulobacter crescentus NA1000

Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate CCNA_00902 CCNA_00902 inositol ABC transporter, periplasmic inositol-binding protein IbpA

Query= CharProtDB::CH_003593
         (296 letters)



>FitnessBrowser__Caulo:CCNA_00902
          Length = 326

 Score =  157 bits (396), Expect = 4e-43
 Identities = 99/308 (32%), Positives = 169/308 (54%), Gaps = 17/308 (5%)

Query: 1   MNMKKLATLVSAVALSA------TVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADK 54
           M+ ++L  L + + L        T  A   A+  + +  + L+ PFFV+++   + EA K
Sbjct: 6   MSRRRLLGLAAGLGLGTAALGLMTGCARGGAEAEVVVSFNDLSQPFFVAMRRELEDEAAK 65

Query: 55  LGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLD 114
           LG  + VLD+QNN +K+++++Q   V+G K++++ PTDS A+  A     +  + VI++D
Sbjct: 66  LGVKVQVLDAQNNSSKQISDLQAAAVQGAKVVIVAPTDSKALAGAADDLVEQGVAVISVD 125

Query: 115 RQATKGE-VVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQA 173
           R    G+  V H+ +DNV GG+   D++ K    GA+V+ +    G+S++ ER +G    
Sbjct: 126 RNIAGGKTAVPHVGADNVAGGRAMADWVVKTYPAGARVVVITNDPGSSSSIERVKGVHDG 185

Query: 174 VAA--HKFNVLASQPADFDRIKGLNVMQNLLTAHPDV--QAVFAQNDEMALGALRALQTA 229
           +AA    F ++  Q A+  R + L V QN+LT+  D     +   ND+MA+GAL A++ A
Sbjct: 186 LAAGGPAFKIVTEQTANSKRDQALTVTQNILTSMRDTPPDVILCLNDDMAMGALEAVRAA 245

Query: 230 G--KSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPD-QIGAKGVETADKVLKGEKVQAKY 286
           G   + V V+GFD  P+    +  G++ AT+ Q P  QI     +  DK+  G  +++  
Sbjct: 246 GLDSAKVKVIGFDAIPEALARIKAGEMVATVEQNPGLQIRTALRQAVDKIKSGAALKS-- 303

Query: 287 PVDLKLVV 294
            V LK V+
Sbjct: 304 -VSLKPVL 310


Lambda     K      H
   0.313    0.129    0.344 

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: 228
Number of extensions: 13
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: 296
Length of database: 326
Length adjustment: 27
Effective length of query: 269
Effective length of database: 299
Effective search space:    80431
Effective search space used:    80431
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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