GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Pseudomonas fluorescens FW300-N2E2

Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Pf6N2E2_2033 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)

Query= TCDB::Q9WXN4
         (268 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2033
          Length = 530

 Score =  159 bits (403), Expect = 9e-44
 Identities = 90/257 (35%), Positives = 159/257 (61%), Gaps = 9/257 (3%)

Query: 4   LVVKNLTKIFSLG---FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60
           L V++L   F L    F  K  + AV  +S  ++  + + +VGESGSGK+T  + ILRL+
Sbjct: 276 LQVQDLRVSFPLSGGLFRRKEYLRAVDGISLSIQRGKTLGIVGESGSGKSTLGQAILRLI 335

Query: 61  PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE 120
             + G I F+G+ +  D   +++L  +R+++  VFQDPF S +P   V++ + + + +  
Sbjct: 336 E-SEGSIRFQGQAL--DHLSQKALRPWRKQMQVVFQDPFGSLSPRMSVQQIISEGLEV-- 390

Query: 121 NKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180
           ++PS+ ++    + ++L  VG+DP     +YPH+ SGGQ+QRI IAR  +L+P LI+ DE
Sbjct: 391 HQPSSPEQCEARVIQALKEVGLDPA-TRHRYPHEFSGGQRQRIAIARALVLKPALILLDE 449

Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPD 240
           PTS +D + +  ++ LL +L+++   + +FI+HDL +   ++ ++ V+K+G++VE+G   
Sbjct: 450 PTSALDRTVQKQVVALLRQLQQKYDLTYLFISHDLAVVRALAHDMIVIKDGKVVEQGASH 509

Query: 241 KVVLEPTHEYTKLLVGS 257
            V   P H YTK L+ +
Sbjct: 510 DVFDSPQHPYTKELLAA 526



 Score =  155 bits (392), Expect = 2e-42
 Identities = 92/241 (38%), Positives = 147/241 (60%), Gaps = 10/241 (4%)

Query: 26  VKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP----TSGEIYFEGKDIWKDIKDR 81
           V+N+  +++  E ++LVGESGSGK+ TA  IL+LLP     TSG I + G+++     D 
Sbjct: 27  VRNLCLDIRPGECLALVGESGSGKSVTAHSILQLLPENEAHTSGSIRYRGQELVG--ADT 84

Query: 82  ESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRV 140
           ++L E R  ++  +FQ+P  S NP + VE+ + + + L  +K    K A + I E L  V
Sbjct: 85  QALRELRGNRIAMIFQEPMTSLNPLHSVEKQIGETLML--HKGLGGKAARQRILELLTLV 142

Query: 141 GI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199
           GI +P + L  YPHQ+SGGQ+QR++IA      P L++ADEPT+ +D + +  I+ LL+ 
Sbjct: 143 GIQNPVERLKAYPHQLSGGQRQRVIIAMALACEPELLIADEPTTALDVTVQRKILLLLKS 202

Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259
           L++  G S++ I+HDL L   ++  + VMK GEIVE+   + +   P H Y+  L+ + P
Sbjct: 203 LQQRLGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCETLFSAPKHPYSCELLHAEP 262

Query: 260 K 260
           +
Sbjct: 263 E 263


Lambda     K      H
   0.319    0.139    0.397 

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: 377
Number of extensions: 16
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 268
Length of database: 530
Length adjustment: 30
Effective length of query: 238
Effective length of database: 500
Effective search space:   119000
Effective search space used:   119000
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 (21.7 bits)
S2: 50 (23.9 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