GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Pseudomonas fluorescens GW456-L13

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PfGW456L13_3031 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031
          Length = 337

 Score =  214 bits (544), Expect = 4e-60
 Identities = 131/306 (42%), Positives = 181/306 (59%), Gaps = 5/306 (1%)

Query: 20  RTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNH 79
           RT L  +   SE LG  I  K E+LQ T +FKIRGA N +        A+GV+TASAGNH
Sbjct: 29  RTPLQPAPALSEALGNQILLKREDLQPTFSFKIRGAYNKLVQLSEVQKARGVVTASAGNH 88

Query: 80  AQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERG 139
           AQGVA +A  LG+ +T+ MP +TP  KV   R  GA+ VL G +F  A A A+    E G
Sbjct: 89  AQGVALAARELGINATIVMPCTTPQLKVIGVRSRGADAVLHGESFPFALACALDLARETG 148

Query: 140 ALFVHPFDDPLVMAGQGTIGLEVL-QELPDVANILVPIGGGGLIAGIATAIRETHPHVRI 198
             FV PFDDP V+AGQGT+ +E+L Q    +  I VP+GGGGLIAGIA  ++   P VR+
Sbjct: 149 RTFVSPFDDPEVIAGQGTVAMEILRQHQGPLDAIFVPVGGGGLIAGIAAYVKYLRPEVRV 208

Query: 199 IGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEE 258
           IGVE+  +     ++  G+ V +P   T ADG+AV + G   F + R  VD+VV V  +E
Sbjct: 209 IGVESEHSACLQAAMHAGERVVLPSVGTFADGVAVAQIGAYGFEVCRFCVDDVVTVSNDE 268

Query: 259 IALAIVALLERTKLLVEGAGAVPLAALLNRRV--TDLSGKT-VCVLSGGNIDVKTISVVV 315
           +  AI  + + T+ + E +GA+ +A  + R V  T   G+T V + SG NI+  ++  V 
Sbjct: 269 LCAAIKNIYDDTRSITEPSGALAVAG-IKRYVAQTGALGQTLVAIDSGANINFDSLGHVA 327

Query: 316 ERGLVA 321
           ER  ++
Sbjct: 328 ERAALS 333


Lambda     K      H
   0.319    0.137    0.383 

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: 289
Number of extensions: 13
Number of successful extensions: 2
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: 402
Length of database: 337
Length adjustment: 30
Effective length of query: 372
Effective length of database: 307
Effective search space:   114204
Effective search space used:   114204
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 (21.8 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