GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pseudomonas fluorescens FW300-N1B4

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate Pf1N1B4_4688 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= curated2:Q9YAW4
         (335 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4688
          Length = 317

 Score =  179 bits (454), Expect = 8e-50
 Identities = 105/261 (40%), Positives = 147/261 (56%), Gaps = 10/261 (3%)

Query: 57  RIDCDLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAA 116
           R D DLL + P L+++    +    +D++ A  LGI V  T      A  E TWALI+AA
Sbjct: 61  RFDEDLLRRLPTLKLLVTGGMRNAALDLKAAAALGIQVCGTDSY-KHAAPELTWALIMAA 119

Query: 117 ARRVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMR 176
            R +V   + +R G+W            LG +L+GKTL ILG+G IG RVA  G+ FGMR
Sbjct: 120 TRNLVAEANALRAGQW---------QQGLGGDLQGKTLAILGLGSIGQRVARFGQVFGMR 170

Query: 177 IIYHSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAI 236
           +I  S +   E   E+   Y S ++L  ++D+LS+HL L++ +R L+    L  MK TA 
Sbjct: 171 VIAWSENLTAERAAEVDVTYVSKQELFEQADVLSVHLVLSERSRGLVDAQALDWMKPTAW 230

Query: 237 LVNTGRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATR 296
           LVNT RG IVD  AL+KAL++  +A AALDVFE EPL  +HP     NV+  PH    +R
Sbjct: 231 LVNTARGPIVDESALIKALQKKRLAGAALDVFEHEPLPRHHPFRTLDNVLATPHVGYVSR 290

Query: 297 ETRLRMAMMAAENLVAFAQGK 317
           +          E++ A+A G+
Sbjct: 291 QNYQLFFSQMIEDIQAWAAGE 311


Lambda     K      H
   0.322    0.136    0.406 

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: 253
Number of extensions: 11
Number of successful extensions: 3
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: 335
Length of database: 317
Length adjustment: 28
Effective length of query: 307
Effective length of database: 289
Effective search space:    88723
Effective search space used:    88723
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 (21.9 bits)
S2: 48 (23.1 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