GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas fluorescens FW300-N2E3

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AO353_02795 AO353_02795 carnitine dehydratase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_02795
          Length = 393

 Score =  201 bits (512), Expect = 2e-56
 Identities = 142/408 (34%), Positives = 206/408 (50%), Gaps = 21/408 (5%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L+ L+VLD S +L GP+A  +LAD+GA+V+++E P   D  R   P        + T+
Sbjct: 3   GPLASLKVLDFSTLLPGPFASLLLADMGAEVLRIESPTRMDLVRVLPP------HDQGTS 56

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
            +  YL  NRNK+S+ +D  +P    +V++L    DIL+E F+ G +   GL Y++LKAI
Sbjct: 57  ASHAYL--NRNKRSLALDLKQPAALEVVKQLLQDHDILLEQFRPGVMERLGLGYEALKAI 114

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+LIY SITG+GQTGPY  RAG+D     L G+ S TG     E +GP+ +GV + DI 
Sbjct: 115 NPRLIYVSITGYGQTGPYKDRAGHDINYLSLAGVSSYTGH----EDSGPLPLGVQVADIA 170

Query: 182 TG-LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
            G L+    +LAA+  R+H G GQH+D+++ D   +  A     YL  G  P R      
Sbjct: 171 GGSLHGVIGLLAAVIAREHSGQGQHLDVSMTDCAFSLNAMAGAGYLACGVTPGREDQMLN 230

Query: 241 NIVPYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299
               Y  + T DG ++     +  F ++     GQP+ A           V  +   + L
Sbjct: 231 GGSFYDYYRTRDGRWMSVGSLEPDFMQQLCTALGQPELA-----VLGLSPVPEQQKALKL 285

Query: 300 IRQATVFK-TTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQV 358
             Q    K   AE  T          P+  LA+    PQ++AR L  ++P        Q+
Sbjct: 286 AFQIEFEKHDFAELCTLFAGLDACVEPVLSLAEAVEHPQLKARDLVTQVPRGDGTAQAQM 345

Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           A P++ SE   E R+    LGEHT +VL   LG     + A R A V+
Sbjct: 346 ACPLKFSEGLPEPRHIGAALGEHTDQVLGE-LGYSAERIEALRRARVV 392


Lambda     K      H
   0.319    0.137    0.408 

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: 415
Number of extensions: 18
Number of successful extensions: 5
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: 406
Length of database: 393
Length adjustment: 31
Effective length of query: 375
Effective length of database: 362
Effective search space:   135750
Effective search space used:   135750
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