GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ibpA in Paraburkholderia bryophila 376MFSha3.1

Align Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate H281DRAFT_04150 H281DRAFT_04150 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= TCDB::B8H228
         (326 letters)



>FitnessBrowser__Burk376:H281DRAFT_04150
          Length = 317

 Score =  124 bits (312), Expect = 2e-33
 Identities = 88/294 (29%), Positives = 148/294 (50%), Gaps = 11/294 (3%)

Query: 24  ALGLMTGCARGGAEAEVVVSFNDLSQPFFVAMRRELEDEAAKLGVKVQVLDAQNNSSKQI 83
           +L ++   A   A  ++ ++F +L+ P+FV M++ L D AA  G  V V DA ++ SKQ+
Sbjct: 27  SLSMIAVPAAQAAPLKIGMTFQELNNPYFVTMQKALNDAAASTGATVIVTDAHHDVSKQV 86

Query: 84  SDLQAAAVQGAKVVIVAPTDSKALAGAADDLVEQGVAVISVDRNIAGGKTAVPHVGADNV 143
           SD++    +   +++V PTDS  +  A     + GV V++VD N  G   +   VG+ N 
Sbjct: 87  SDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANANGPVDS--FVGSKNF 144

Query: 144 AGGRAMADWVVKTYPAGARVVVITNDPGSSSSIERVKGVHDGLAAGGPAFKIVTEQTANS 203
             G+   +++ K+      V ++   P     +ERV+G    LA   P  K+V  Q    
Sbjct: 145 DAGQMACEYLSKSIGGSGEVAILDGIP-VVPILERVRGCKAALAK-SPGVKLVDTQNGKQ 202

Query: 204 KRDQALTVTQNILTSMRDTPPDVILCLNDDMAMGALEAVRAAGLDSAKVKVIGFDAIPEA 263
           +R  AL+VT+N++ +  +     +  +ND  +MGAL A+ ++G D   +K+   D  PEA
Sbjct: 203 ERATALSVTENMIQAHPNLKG--VFSVNDGGSMGALSAIESSGKD---IKLTSVDGAPEA 257

Query: 264 LARIKA--GEMVATVEQNPGLQIRTALRQAVDKIKSGAALKSVSLKPVLITSGN 315
           +A I+    + V T  Q P  Q+R AL  A  K       K++ +   +I   N
Sbjct: 258 IAAIQKPNSKFVETSAQFPADQVRIALGIAYAKKWGANVPKAIPVDVKMIDKSN 311


Lambda     K      H
   0.315    0.130    0.353 

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: 209
Number of extensions: 9
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: 326
Length of database: 317
Length adjustment: 28
Effective length of query: 298
Effective length of database: 289
Effective search space:    86122
Effective search space used:    86122
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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