GapMind for catabolism of small carbon sources

 

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

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate H281DRAFT_03224 H281DRAFT_03224 mannose ABC transporter ATP-binding protein /fructose ABC transporter ATP-binding protein /ribose ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Burk376:H281DRAFT_03224
          Length = 265

 Score =  336 bits (862), Expect = 3e-97
 Identities = 173/255 (67%), Positives = 208/255 (81%), Gaps = 1/255 (0%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           P+L ARGLVKRYG VTALD  DF++ PGEILAVIGDNGAGKSS+IKA+SGA  PDEGEI 
Sbjct: 12  PVLQARGLVKRYGNVTALDGCDFEVLPGEILAVIGDNGAGKSSLIKALSGATVPDEGEIL 71

Query: 65  LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124
           L+GKP++FRSP++AR  GIETVYQ LA++PA+SIA+N+FL RE+ KPG  G  F+ +D+ 
Sbjct: 72  LDGKPVKFRSPLDARAQGIETVYQELAVAPAMSIAENLFLARELVKPGWRGSIFKMIDKR 131

Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184
            M ++A A + +L +  I+++ QAVETLSGGQRQGVAVAR+AAF   VVI+DEPTAALGV
Sbjct: 132 RMLEEATAHMKDLQI-GIRSMRQAVETLSGGQRQGVAVARSAAFARHVVILDEPTAALGV 190

Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244
           KE   VLELI  VR RGLP++LISHNMPHVFEVADRIHI RLGRR  ++N KD  MS+AV
Sbjct: 191 KEGNMVLELIRRVRDRGLPVILISHNMPHVFEVADRIHIQRLGRRAALVNTKDVHMSEAV 250

Query: 245 AFMTGAKEPPREAIA 259
           A MTGAKE   +AIA
Sbjct: 251 AIMTGAKEADVKAIA 265


Lambda     K      H
   0.321    0.136    0.383 

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: 230
Number of extensions: 4
Number of successful extensions: 2
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: 260
Length of database: 265
Length adjustment: 25
Effective length of query: 235
Effective length of database: 240
Effective search space:    56400
Effective search space used:    56400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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