GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Pseudomonas fluorescens FW300-N2C3

Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate AO356_25560 AO356_25560 2-keto-3-deoxy-L-rhamnonate aldolase

Query= SwissProt::Q47098
         (262 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25560
          Length = 265

 Score =  352 bits (903), Expect = e-102
 Identities = 174/260 (66%), Positives = 208/260 (80%)

Query: 3   NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62
           N+FK  L++G  QIGLWLGL+ +Y AEL A AGFDWLLIDGEHAPN+++T+L QLQA+AP
Sbjct: 6   NTFKQRLRSGEAQIGLWLGLADAYCAELAANAGFDWLLIDGEHAPNDLRTLLGQLQAVAP 65

Query: 63  YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122
           YP QPV+RP   D   IKQ+LD+G QTLLVPMV++A++ARE VRA  YPP G+RGVGSAL
Sbjct: 66  YPGQPVIRPVVGDTALIKQVLDIGVQTLLVPMVESAEQARELVRAIHYPPQGVRGVGSAL 125

Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182
           ARASRWN IP YL KA++QMC+LVQIE+RE + NL  I  VEGVDGVFIGPADLSA MG+
Sbjct: 126 ARASRWNSIPGYLDKADEQMCLLVQIESREGLANLDAIAAVEGVDGVFIGPADLSASMGF 185

Query: 183 AGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARA 242
            GNP HP+VQAAIE AI +IR++GKA GIL A+E+LA+RY+ELGA FVAVGVDTT+L R 
Sbjct: 186 RGNPGHPQVQAAIEDAIARIRQAGKAAGILSADEKLARRYIELGAAFVAVGVDTTVLMRG 245

Query: 243 AEALAARFGAQATAVKPGVY 262
            + LAA F         GVY
Sbjct: 246 LQTLAATFKDTPKPAAGGVY 265


Lambda     K      H
   0.317    0.133    0.387 

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: 269
Number of extensions: 4
Number of successful extensions: 1
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: 262
Length of database: 265
Length adjustment: 25
Effective length of query: 237
Effective length of database: 240
Effective search space:    56880
Effective search space used:    56880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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