GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Pseudomonas putida KT2440

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate PP_0654 PP_0654 putative malate dehydrogenase

Query= BRENDA::Q9GT92
         (321 letters)



>FitnessBrowser__Putida:PP_0654
          Length = 310

 Score =  207 bits (527), Expect = 3e-58
 Identities = 114/302 (37%), Positives = 174/302 (57%), Gaps = 6/302 (1%)

Query: 6   KIAVIGSGQIGGNIAYIVGKDNLA-DVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGT 64
           K+ ++G+G +G   A I+ +D L  ++VL D+   + QGKALD+  + V  GS + V G 
Sbjct: 4   KLTIVGAGLVGEAAAQIIARDELCRELVLMDVQGELAQGKALDVWQAAVDSGSDTHVHGG 63

Query: 65  NDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPL 124
                + GS++V+ITA +P +P   R ++L  N  ILDS+   +K + P A V+ ++NP+
Sbjct: 64  AKAEMLEGSELVVITAGVPRKPGQSRQDVLSTNLPILDSIMADIKHHAPTATVLVVSNPV 123

Query: 125 DVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPV 184
           DV+      VSG   +KV G AGVLD++R + FIA+  G +A D++A V+GGHGD MVP+
Sbjct: 124 DVLTYRAWSVSGQGRDKVFGQAGVLDTARMKCFIAEQTGFSARDITALVLGGHGDSMVPL 183

Query: 185 TSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMA 244
                +G VPLS F     ++ EQI++IV  TR    E+    KTG+A  AP  A  +M 
Sbjct: 184 MRYCQIGSVPLSHF-----LSSEQIEQIVERTRKGGGEILGLKKTGSACDAPGVAIAQMV 238

Query: 245 EAYLKDRKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLKQKLLGESIN 304
           +A    R  ++P  A     YG   I MGVP ++ + G+  I+EL L   +Q +   S +
Sbjct: 239 DAIANGRNRILPAVAILEGEYGRTDIAMGVPCVLAEKGLARIIELPLDAQEQAMFDHSAD 298

Query: 305 EV 306
           +V
Sbjct: 299 QV 300


Lambda     K      H
   0.319    0.136    0.394 

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: 246
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: 321
Length of database: 310
Length adjustment: 27
Effective length of query: 294
Effective length of database: 283
Effective search space:    83202
Effective search space used:    83202
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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