GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas stutzeri RCH2

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF2609 Psest_2660 Predicted acyl-CoA transferases/carnitine dehydratase

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



>FitnessBrowser__psRCH2:GFF2609
          Length = 400

 Score =  241 bits (615), Expect = 3e-68
 Identities = 152/406 (37%), Positives = 222/406 (54%), Gaps = 19/406 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  L+V+++ +++AGP+A ++L + GADVIK+E P  GD  R W    LKD        +
Sbjct: 11  LQGLKVIEMGQLIAGPFASKLLGEFGADVIKIEPPKVGDPLRKWRK--LKDGT------S 62

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            ++   +RNK+SVT+D    EGQ +VR+L A++DIL+ENF+ G L  +GL +D L  +NP
Sbjct: 63  LWWHVQSRNKRSVTLDLKAAEGQAIVRQLVAEADILVENFRPGTLEEWGLGWDELSKLNP 122

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +LI   I+G+GQTGPY    G+  + + +GGL  L+G P    G  PV+VGV++ D L+ 
Sbjct: 123 RLIMLRISGYGQTGPYRDLPGFGVIGEAMGGLRHLSGYP----GQPPVRVGVSIGDSLSS 178

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           LY    +L AL  R+  G GQ ID+AL +   A + +    Y   G   +  G+A P I 
Sbjct: 179 LYGVIGVLLALQERNRSGQGQEIDVALYESVFAMMESLVPEYDAFGYVREPAGSALPGIT 238

Query: 244 PYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302
           P   +P  DG ++L  GN D  +++   + G+   ADDPRFA N  R  +  ++   I +
Sbjct: 239 PSNSYPCNDGAYVLIAGNGDSIYKRLMTLMGRQDLADDPRFAHNDGRAQHAELIDAAIGE 298

Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAG--KVPQVAS 360
            T+     E +  L+ A VP G     A +  DP   AR + +E     AG  KVP V  
Sbjct: 299 WTIQHGRDEVIEALKGARVPAGYPYTAADIVKDPHYLARQM-IEQVQTFAGPLKVPGVLP 357

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
             +LS TP       P LGEHT +VL   LGL +      RE G++
Sbjct: 358 --KLSRTPGRIGEGGPQLGEHTDDVLAG-LGLTDEQRQGLRERGII 400


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: 494
Number of extensions: 22
Number of successful extensions: 6
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: 400
Length adjustment: 31
Effective length of query: 375
Effective length of database: 369
Effective search space:   138375
Effective search space used:   138375
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