GapMind for catabolism of small carbon sources

 

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

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Pf6N2E2_3801 Histidine ABC transporter, ATP-binding protein (TC 3.A.1)

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3801
          Length = 276

 Score =  310 bits (795), Expect = 2e-89
 Identities = 155/261 (59%), Positives = 206/261 (78%)

Query: 4   KLEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLS 63
           K+E+KN++KIFG   + A + I Q  +K+Q+L +TG  +GV D SL+I  GEIFVIMGLS
Sbjct: 8   KIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLS 67

Query: 64  GSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTV 123
           GSGKST+VR  NRLI+PT G +L+DG DI ++    LRE RR KI+MVFQSF L+PH +V
Sbjct: 68  GSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSV 127

Query: 124 LDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINP 183
           LDN A+G+++ G + +   E+AL  +  VGL+ Y + YP +LSGGMRQRVGLARALA + 
Sbjct: 128 LDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADT 187

Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243
           DI+LMDEAFSALDPLIR EMQD+L++LQ    +TIVFI+HDLDEA+RIG+RIAI+++G++
Sbjct: 188 DIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKL 247

Query: 244 VQVGTPDEILNNPANDYVRTF 264
           +QVGTP EIL++PA++YV  F
Sbjct: 248 IQVGTPREILHSPADEYVDRF 268


Lambda     K      H
   0.319    0.137    0.378 

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: 341
Number of extensions: 19
Number of successful extensions: 1
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: 400
Length of database: 276
Length adjustment: 28
Effective length of query: 372
Effective length of database: 248
Effective search space:    92256
Effective search space used:    92256
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: 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