GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Burkholderia phytofirmans PsJN

Align Ribose import permease protein RbsC (characterized)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease

Query= SwissProt::P0AGI1
         (321 letters)



>FitnessBrowser__BFirm:BPHYT_RS20745
          Length = 341

 Score =  236 bits (603), Expect = 5e-67
 Identities = 134/321 (41%), Positives = 200/321 (62%), Gaps = 7/321 (2%)

Query: 4   QTVSG--RRYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAV 61
           +T SG   R FT   L +  +  +L++L+   S  SP F  ++N+  ILQ T+VN ++A+
Sbjct: 14  KTFSGLRARVFTPTALQKLLAFGSLILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAI 73

Query: 62  GMTLVILTSGIDLSVGSLLALTGAVAASIVGI-EVNALVAVAAALALGAAIGAVTGVIVA 120
             T VI+T GIDLSVG+L+  T  +    +    +     V AA+  GA  G V+G + A
Sbjct: 74  ACTFVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTA 133

Query: 121 KGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPL--GVPTPVWI 178
           K ++  FIATL MM+LL+G+++V +   P+    TEN  +     +   L   +P P  +
Sbjct: 134 KMKIPPFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAV 193

Query: 179 MGIVFLA--AWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGI 236
           + + FLA  +   L+ T LGRY +ALG NE A RLSG+NV++ KI +Y L G +  +AG+
Sbjct: 194 LILFFLAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGL 253

Query: 237 IEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLG 296
           +  +RL+SAQP  G GYEL+AIAAVV+GGTSL+GG G I+GT+IGA I+  L NGL ++ 
Sbjct: 254 LIASRLNSAQPALGQGYELEAIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMS 313

Query: 297 VSSYYQMIVKAVVILLAVLVD 317
           V+  +Q++V  ++I+LAV  D
Sbjct: 314 VAQEWQIVVTGLIIILAVYGD 334


Lambda     K      H
   0.324    0.139    0.393 

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: 250
Number of extensions: 12
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: 321
Length of database: 341
Length adjustment: 28
Effective length of query: 293
Effective length of database: 313
Effective search space:    91709
Effective search space used:    91709
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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