GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Acidovorax sp. GW101-3H11

Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39 (characterized)
to candidate Ac3H11_3372 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)

Query= SwissProt::O05151
         (258 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3372
          Length = 277

 Score =  309 bits (792), Expect = 3e-89
 Identities = 154/262 (58%), Positives = 194/262 (74%), Gaps = 10/262 (3%)

Query: 1   MQSPINSFKKALAEGRTQIGFWLALGDAYSAEVCAGAGFDWLLIDGEHAPQDLRSVLAQL 60
           M +P NSFK+ALA+G  QIG WL L DAY+AE+ AG G+DWLL+DGEHAP DLRS+L QL
Sbjct: 1   MHTPTNSFKQALAQGEAQIGLWLGLADAYTAEILAGTGYDWLLVDGEHAPNDLRSILHQL 60

Query: 61  QVIGAY--------RDCHAAVRVPSADTTVIKQYLDLGAQSLLVPMVDTADEAAAVVRAC 112
           Q I +         R  HA  RVP  DT +IKQYLD+GAQ+LLVPMVDT ++A  +VRA 
Sbjct: 61  QAIASASSALPPGARASHAVARVPVGDTALIKQYLDIGAQTLLVPMVDTPEQAQQLVRAT 120

Query: 113 RYPPGGIRGVGGA--RASRWGRYPRYLHEADEQVCVVVQAETALALSNLEAIAEVDGIDG 170
           RY P G+RG+G A  R+SRW  YPRY+HEA++Q+C++VQAET  A+++L+AIA   G+DG
Sbjct: 121 RYAPEGVRGMGSALARSSRWQAYPRYVHEANQQICLLVQAETVEAMAHLDAIAATPGVDG 180

Query: 171 VFIGTADLAASLGFPGNPAHPEVQDAILDALQRVRAAGKAPGVLTPVEDLAQKYLAHGAV 230
           VFIG ADL+AS+G PGNP HP+VQ AI D + R+  AGKAPG+L   E  A+++LA GA+
Sbjct: 181 VFIGPADLSASMGHPGNPGHPDVQAAIHDGIARILRAGKAPGILATNEAQARQWLAAGAL 240

Query: 231 FVAVGIDTHLLAKQTSALAARF 252
           FVAVG+DT LL      L ARF
Sbjct: 241 FVAVGVDTMLLTSAAQNLLARF 262


Lambda     K      H
   0.320    0.135    0.400 

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: 280
Number of extensions: 14
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: 258
Length of database: 277
Length adjustment: 25
Effective length of query: 233
Effective length of database: 252
Effective search space:    58716
Effective search space used:    58716
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: 47 (22.7 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